Fri Mar 18 11:59:31 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/bin/recon-all -subject Freesurfer -i /tmp/surfaKCaG0free/MRI/0120-1.3.12.2.1107.5.2.32.35235.30000012012913052305400013450.dcm -all subjid Freesurfer setenv SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Actual FREESURFER_HOME /net/tautona/neuro/arch/Linux64/packages/freesurfer/stable-5.3 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux rc-russia 3.14.8-mosix #1 SMP Thu Jun 19 12:56:58 EDT 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 773245 maxlocks unlimited maxsignal 773245 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 98995712 26913512 72082200 1036 296088 7527488 -/+ buffers/cache: 19089936 79905776 Swap: 37737468 71020 37666448 ######################################## 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: 2016/03/18-15:59:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix 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: 2016/03/18-15:59:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix 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: 2016/03/18-15:59:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:31-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix 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: 2016/03/18-15:59:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix 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: 2016/03/18-15:59:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/03/18-15:59:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: rudolphpienaar Machine: rc-russia Platform: Linux PlatformVersion: 3.14.8-mosix CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /tmp/surfaKCaG0free/MRI/Freesurfer mri_convert /tmp/surfaKCaG0free/MRI/0120-1.3.12.2.1107.5.2.32.35235.30000012012913052305400013450.dcm /tmp/surfaKCaG0free/MRI/Freesurfer/mri/orig/001.mgz mri_convert /tmp/surfaKCaG0free/MRI/0120-1.3.12.2.1107.5.2.32.35235.30000012012913052305400013450.dcm /tmp/surfaKCaG0free/MRI/Freesurfer/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /tmp/surfaKCaG0free/MRI/0120-1.3.12.2.1107.5.2.32.35235.30000012012913052305400013450.dcm... Getting Series No INFO: Found 177 files in /tmp/surfaKCaG0free/MRI INFO: Scanning for Series Number 100 Scanning Directory INFO: found 168 files in series INFO: loading series header info. RunNo = 99 INFO: sorting. WARNING: file /tmp/surfaKCaG0free/MRI/0167-1.3.12.2.1107.5.2.32.35235.30000012012913052305400013497.dcm does not contain a Siemens ASCII header has this file been anonymized? Proceeding as best as I can ... INFO: (192 192 168), nframes = 1, ismosaic=0 PE Dir ROW ROW FileName /tmp/surfaKCaG0free/MRI/0167-1.3.12.2.1107.5.2.32.35235.30000012012913052305400013497.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName ARIASBAEZ^LUZNELI Date and time StudyDate 20120130 StudyTime 132026 SeriesTime 133211.291000 AcqTime 132308.062500 Acquisition parameters PulseSeq r73d4_ns Protocol mocoMEMPRAGE_192FOV PhEncDir ROW EchoNo 1 FlipAngle 7 EchoTime 1.74 InversionTime -1 RepetitionTime 2530 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 99 SeriesNo 100 ImageNo 167 NImageRows 192 NImageCols 192 NFrames 1 SliceArraylSize 0 IsMosaic 0 ImgPos 90.5844 101.9466 91.7508 VolRes 1.0000 1.0000 1.0000 VolDim 192 192 168 Vc -0.9998 -0.0126 -0.0142 Vr 0.0114 -0.9964 0.0841 Vs 0.0152 -0.0840 -0.9964 VolCenter -3.0287 -1.9707 14.7717 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=1.74, TI=-1.00, flip angle=7.00 i_ras = (-0.99982, -0.012624, -0.0141853) j_ras = (0.0113871, -0.99639, 0.0841296) k_ras = (0.0151961, -0.0839529, -0.996354) writing to /tmp/surfaKCaG0free/MRI/Freesurfer/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Fri Mar 18 12:00:33 EDT 2016 Found 1 runs /tmp/surfaKCaG0free/MRI/Freesurfer/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 /tmp/surfaKCaG0free/MRI/Freesurfer/mri/orig/001.mgz /tmp/surfaKCaG0free/MRI/Freesurfer/mri/rawavg.mgz /tmp/surfaKCaG0free/MRI/Freesurfer mri_convert /tmp/surfaKCaG0free/MRI/Freesurfer/mri/rawavg.mgz /tmp/surfaKCaG0free/MRI/Freesurfer/mri/orig.mgz --conform mri_convert /tmp/surfaKCaG0free/MRI/Freesurfer/mri/rawavg.mgz /tmp/surfaKCaG0free/MRI/Freesurfer/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /tmp/surfaKCaG0free/MRI/Freesurfer/mri/rawavg.mgz... TR=2530.00, TE=1.74, TI=-1.00, flip angle=7.00 i_ras = (-0.99982, -0.012624, -0.0141853) j_ras = (0.0113871, -0.99639, 0.0841296) k_ras = (0.0151961, -0.0839529, -0.996354) Original Data has (1, 1, 1) mm size and (192, 192, 168) 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 /tmp/surfaKCaG0free/MRI/Freesurfer/mri/orig.mgz... mri_add_xform_to_header -c /tmp/surfaKCaG0free/MRI/Freesurfer/mri/transforms/talairach.xfm /tmp/surfaKCaG0free/MRI/Freesurfer/mri/orig.mgz /tmp/surfaKCaG0free/MRI/Freesurfer/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Fri Mar 18 12:00:41 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/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 Mar 18 12:01:58 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5550, pval=0.2115 >= threshold=0.0050) awk -f /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/bin/extract_talairach_avi_QA.awk /tmp/surfaKCaG0free/MRI/Freesurfer/mri/transforms/talairach_avi.log tal_QC_AZS /tmp/surfaKCaG0free/MRI/Freesurfer/mri/transforms/talairach_avi.log TalAviQA: 0.97371 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Fri Mar 18 12:01:58 EDT 2016 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /tmp/surfaKCaG0free/MRI/Freesurfer/mri /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/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 rc-russia 3.14.8-mosix #1 SMP Thu Jun 19 12:56:58 EDT 2014 x86_64 x86_64 x86_64 GNU/Linux Fri Mar 18 12:01:58 EDT 2016 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.6059 /tmp/surfaKCaG0free/MRI/Freesurfer/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.6059/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.6059/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=1.74, TI=-1.00, flip angle=7.00 i_ras = (-1, -1.62981e-09, -9.31323e-10) j_ras = (-9.31323e-10, 0, -1) k_ras = (2.67755e-09, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.6059/nu0.mnc... -------------------------------------------------------- Iteration 1 Fri Mar 18 12:02:00 EDT 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.6059/nu0.mnc ./tmp.mri_nu_correct.mni.6059/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.6059/0/ defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [rudolphpienaar@rc-russia:/tmp/surfaKCaG0free/MRI/Freesurfer/mri/] [2016-03-18 12:02:00] running: /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/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.6059/0/ ./tmp.mri_nu_correct.mni.6059/nu0.mnc ./tmp.mri_nu_correct.mni.6059/nu1.imp Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 26 CV of field change: 0.000916643 [rudolphpienaar@rc-russia:/tmp/surfaKCaG0free/MRI/Freesurfer/mri/] [2016-03-18 12:02:14] running: /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.6059/nu0.mnc ./tmp.mri_nu_correct.mni.6059/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Fri Mar 18 12:02:17 EDT 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.6059/nu1.mnc ./tmp.mri_nu_correct.mni.6059/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.6059/1/ defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [rudolphpienaar@rc-russia:/tmp/surfaKCaG0free/MRI/Freesurfer/mri/] [2016-03-18 12:02:17] running: /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/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.6059/1/ ./tmp.mri_nu_correct.mni.6059/nu1.mnc ./tmp.mri_nu_correct.mni.6059/nu2.imp Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 22 CV of field change: 0.000921915 [rudolphpienaar@rc-russia:/tmp/surfaKCaG0free/MRI/Freesurfer/mri/] [2016-03-18 12:02:24] running: /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.6059/nu1.mnc ./tmp.mri_nu_correct.mni.6059/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.6059/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.6059/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /tmp/surfaKCaG0free/MRI/Freesurfer/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.6059/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.6059/ones.mgz sysname Linux hostname rc-russia machine x86_64 user rudolphpienaar input ./tmp.mri_nu_correct.mni.6059/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.6059/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.6059/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.6059/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6059/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.6059/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.6059/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6059/input.mean.dat sysname Linux hostname rc-russia machine x86_64 user rudolphpienaar UseRobust 0 Loading ./tmp.mri_nu_correct.mni.6059/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.6059/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.6059/ones.mgz --i ./tmp.mri_nu_correct.mni.6059/nu2.mnc --sum ./tmp.mri_nu_correct.mni.6059/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6059/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.6059/ones.mgz --i ./tmp.mri_nu_correct.mni.6059/nu2.mnc --sum ./tmp.mri_nu_correct.mni.6059/sum.junk --avgwf ./tmp.mri_nu_correct.mni.6059/output.mean.dat sysname Linux hostname rc-russia machine x86_64 user rudolphpienaar UseRobust 0 Loading ./tmp.mri_nu_correct.mni.6059/ones.mgz Loading ./tmp.mri_nu_correct.mni.6059/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.6059/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.6059/nu2.mnc ./tmp.mri_nu_correct.mni.6059/nu2.mnc mul .82590650575669302261 Saving result to './tmp.mri_nu_correct.mni.6059/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.6059/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.6059/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.6059/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.62981e-09, -9.31322e-10) j_ras = (-9.31323e-10, 0, -1) k_ras = (2.67755e-09, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 7 seconds. mapping ( 7, 24) to ( 3, 110) Fri Mar 18 12:03:05 EDT 2016 mri_nu_correct.mni done mri_add_xform_to_header -c /tmp/surfaKCaG0free/MRI/Freesurfer/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Fri Mar 18 12:03:06 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.188 -0.029 0.024 3.099; 0.015 1.179 -0.098 -9.037; -0.022 0.125 1.201 -32.910; 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 = 14 Starting OpenSpline(): npoints = 14 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 91 gm peak at 71 (71), valley at 36 (36) csf peak at 10, setting threshold to 50 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 91 gm peak at 70 (70), valley at 35 (35) csf peak at 10, setting threshold to 50 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 20 seconds. #-------------------------------------------- #@# Skull Stripping Fri Mar 18 12:05:27 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/mri mri_em_register -skull nu.mgz /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/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 '/neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/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=26.0 skull bounding box = (62, 47, 47) --> (194, 213, 208) using (106, 102, 128) as brain centroid... mean wm in atlas = 126, using box (90,82,108) --> (122, 122,147) to find MRI wm before smoothing, mri peak at 111 after smoothing, mri peak at 110, scaling input intensities by 1.145 scaling channel 0 by 1.14545 initial log_p = -4.9 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.850645 @ (9.091, -9.091, -45.455) max log p = -4.804714 @ (-13.636, 4.545, 22.727) max log p = -4.794583 @ (2.273, -6.818, -6.818) max log p = -4.777174 @ (-1.136, 1.136, 5.682) max log p = -4.768775 @ (1.705, -1.705, -5.114) max log p = -4.768775 @ (0.000, 0.000, 0.000) Found translation: (-1.7, -11.9, -29.0): log p = -4.769 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.8 (thresh=-4.8) 1.236 0.000 0.000 -31.818; 0.000 1.226 -0.161 5.422; 0.000 0.161 1.226 -59.532; 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 =-4.1 (thresh=-4.1) 1.236 0.000 0.000 -31.818; 0.000 1.304 -0.172 -1.953; 0.000 0.173 1.318 -79.450; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.236 0.000 0.000 -31.818; 0.000 1.304 -0.172 -1.953; 0.000 0.173 1.318 -79.450; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.212 -0.044 0.003 -26.161; 0.040 1.335 -0.087 -23.117; 0.000 0.089 1.350 -70.519; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.190 0.003 0.043 -33.449; 0.000 1.336 -0.088 -17.883; -0.039 0.089 1.324 -64.113; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.190 0.023 0.020 -31.877; -0.019 1.337 -0.110 -11.879; -0.019 0.111 1.323 -68.947; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.193 0.023 0.020 -32.246; -0.019 1.342 -0.111 -12.347; -0.019 0.111 1.323 -68.947; 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 1.19281 0.02296 0.01992 -32.24639; -0.01893 1.34195 -0.11072 -12.34694; -0.01945 0.11096 1.32274 -68.94669; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.19281 0.02296 0.01992 -32.24639; -0.01893 1.34195 -0.11072 -12.34694; -0.01945 0.11096 1.32274 -68.94669; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.193 0.023 0.020 -32.246; -0.019 1.342 -0.111 -12.347; -0.019 0.111 1.323 -68.947; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.0 (old=-4.9) transform before final EM align: 1.193 0.023 0.020 -32.246; -0.019 1.342 -0.111 -12.347; -0.019 0.111 1.323 -68.947; 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 1.19281 0.02296 0.01992 -32.24639; -0.01893 1.34195 -0.11072 -12.34694; -0.01945 0.11096 1.32274 -68.94669; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.19281 0.02296 0.01992 -32.24639; -0.01893 1.34195 -0.11072 -12.34694; -0.01945 0.11096 1.32274 -68.94669; 0.00000 0.00000 0.00000 1.00000; dfp_em_step_func: 010: -log(p) = 4.4 after pass:transform: ( 1.19, 0.02, 0.02, -32.25) ( -0.02, 1.34, -0.11, -12.35) ( -0.02, 0.11, 1.32, -68.95) IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESpass 2 through quasi-newton minimization... IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 012: -log(p) = 4.4 tol 0.000000 final transform: 1.193 0.023 0.020 -32.246; -0.019 1.342 -0.111 -12.347; -0.019 0.111 1.323 -68.947; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 30 minutes and 18 seconds. mri_watershed -T1 -brain_atlas /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/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=124 y=107 z=134 r=67 first estimation of the main basin volume: 1265806 voxels Looking for seedpoints 2 found in the cerebellum 9 found in the rest of the brain global maximum in x=103, y=92, z=125, Imax=255 CSF=22, 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=7196697533 voxels, voxel volume =1.000 = 7196697533 mmm3 = 7196697.600 cm3 done. PostAnalyze...Basin Prior 17 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=127,y=108, z=122, r=9659 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 45871 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1054355863 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1054641310 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = -1067672888 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 1066832334 OTHER CSF_MIN=0, CSF_intensity=2, CSF_MAX=4 , nb = 1075913076 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 4, 9, 49, 64 after analyzing : 4, 35, 49, 42 RIGHT_CER before analyzing : 4, 4, 24, 69 after analyzing : 4, 18, 25, 30 LEFT_CER before analyzing : 4, 6, 44, 72 after analyzing : 4, 31, 44, 41 RIGHT_BRAIN before analyzing : 4, 9, 49, 65 after analyzing : 4, 35, 49, 42 LEFT_BRAIN before analyzing : 4, 7, 48, 69 after analyzing : 4, 34, 48, 42 OTHER before analyzing : 4, 9, 51, 65 after analyzing : 4, 37, 51, 44 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...55 iterations *********************VALIDATION********************* curvature mean = -0.015, std = 0.009 curvature mean = 64.282, std = 5.945 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 6.90, sigma = 10.55 after rotation: sse = 6.90, sigma = 10.55 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 7.71, its var is 9.88 before Erosion-Dilatation 6.22% of inacurate vertices after Erosion-Dilatation 4.42% 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...29 iterations mri_strip_skull: done peeling brain Brain Size = 1206968 voxels, voxel volume = 1.000 mm3 = 1206968 mmm3 = 1206.968 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------- #@# EM Registration Fri Mar 18 12:36:06 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/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 '/neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/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=25.0 skull bounding box = (64, 54, 52) --> (189, 155, 201) using (106, 88, 127) as brain centroid... mean wm in atlas = 107, using box (91,76,109) --> (121, 100,145) to find MRI wm before smoothing, mri peak at 111 after smoothing, mri peak at 110, scaling input intensities by 0.973 scaling channel 0 by 0.972727 initial log_p = -4.4 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.334044 @ (-9.091, 9.091, -9.091) max log p = -4.285542 @ (4.545, 4.545, 4.545) max log p = -4.283108 @ (2.273, -2.273, 2.273) max log p = -4.254593 @ (-1.136, 1.136, -1.136) max log p = -4.253305 @ (-0.568, -1.705, 0.568) max log p = -4.253305 @ (0.000, 0.000, 0.000) Found translation: (-4.0, 10.8, -2.8): log p = -4.253 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.8, old_max_log_p =-4.3 (thresh=-4.2) 1.150 0.000 0.000 -23.595; 0.000 1.226 -0.161 1.757; 0.000 0.150 1.140 -49.095; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-3.8, old_max_log_p =-3.8 (thresh=-3.8) 1.150 0.000 0.000 -23.595; 0.000 1.226 -0.161 1.757; 0.000 0.150 1.140 -49.095; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 2 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.6, old_max_log_p =-3.8 (thresh=-3.8) 1.170 0.048 0.031 -33.321; -0.038 1.288 -0.212 9.634; -0.038 0.189 1.134 -47.953; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-3.6, old_max_log_p =-3.6 (thresh=-3.6) 1.170 0.048 0.031 -33.321; -0.038 1.288 -0.212 9.634; -0.038 0.189 1.134 -47.953; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 4 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.6, old_max_log_p =-3.6 (thresh=-3.6) 1.167 0.044 0.003 -29.488; -0.039 1.288 -0.184 6.281; -0.008 0.158 1.135 -48.562; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.6, old_max_log_p =-3.6 (thresh=-3.6) 1.167 0.044 0.003 -29.488; -0.039 1.285 -0.184 6.544; -0.008 0.157 1.133 -48.201; 0.000 0.000 0.000 1.000; min search scale 0.025000 reached *********************************************** Computing MAP estimate using 2772 samples... *********************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-05 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.16675 0.04413 0.00312 -29.48752; -0.03868 1.28508 -0.18360 6.54437; -0.00806 0.15724 1.13255 -48.20116; 0.00000 0.00000 0.00000 1.00000; nsamples 2772 Quasinewton: input matrix 1.16675 0.04413 0.00312 -29.48752; -0.03868 1.28508 -0.18360 6.54437; -0.00806 0.15724 1.13255 -48.20116; 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: 1.167 0.044 0.003 -29.488; -0.039 1.285 -0.184 6.544; -0.008 0.157 1.133 -48.201; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.6 (old=-4.4) transform before final EM align: 1.167 0.044 0.003 -29.488; -0.039 1.285 -0.184 6.544; -0.008 0.157 1.133 -48.201; 0.000 0.000 0.000 1.000; ************************************************** EM alignment process ... Computing final MAP estimate using 312841 samples. ************************************************** dt = 5.00e-06, momentum=0.80, tol=1.00e-07 l_intensity = 1.0000 Aligning input volume to GCA... Transform matrix 1.16675 0.04413 0.00312 -29.48752; -0.03868 1.28508 -0.18360 6.54437; -0.00806 0.15724 1.13255 -48.20116; 0.00000 0.00000 0.00000 1.00000; nsamples 312841 Quasinewton: input matrix 1.16675 0.04413 0.00312 -29.48752; -0.03868 1.28508 -0.18360 6.54437; -0.00806 0.15724 1.13255 -48.20116; 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) = 3.9 tol 0.000000 final transform: 1.167 0.044 0.003 -29.488; -0.039 1.285 -0.184 6.544; -0.008 0.157 1.133 -48.201; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach.lta... registration took 20 minutes and 28 seconds. #-------------------------------------- #@# CA Normalize Fri Mar 18 12:56:34 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/mri mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/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 '/neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/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=25.0 skull bounding box = (64, 54, 52) --> (189, 155, 201) using (106, 88, 127) as brain centroid... mean wm in atlas = 107, using box (91,76,109) --> (121, 100,145) to find MRI wm before smoothing, mri peak at 111 after smoothing, mri peak at 110, scaling input intensities by 0.973 scaling channel 0 by 0.972727 using 244171 sample points... INFO: compute sample coordinates transform 1.167 0.044 0.003 -29.488; -0.039 1.285 -0.184 6.544; -0.008 0.157 1.133 -48.201; 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 (127, 56, 50) --> (185, 151, 198) Left_Cerebral_White_Matter: limiting intensities to 86.0 --> 248.0 0 of 476 (0.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (73, 55, 52) --> (129, 150, 198) Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 248.0 0 of 647 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 116, 67) --> (170, 152, 115) Left_Cerebellum_White_Matter: limiting intensities to 94.0 --> 248.0 0 of 73 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (88, 116, 65) --> (129, 151, 115) Right_Cerebellum_White_Matter: limiting intensities to 100.0 --> 248.0 0 of 39 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 116, 94) --> (142, 167, 125) Brain_Stem: limiting intensities to 97.0 --> 248.0 0 of 49 (0.0%) samples deleted using 1284 total control points for intensity normalization... bias field = 1.016 +- 0.094 0 of 1284 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (127, 56, 50) --> (185, 151, 198) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 121.0 1 of 378 (0.3%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (73, 55, 52) --> (129, 150, 198) Right_Cerebral_White_Matter: limiting intensities to 98.0 --> 255.0 0 of 479 (0.0%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 116, 67) --> (170, 152, 115) Left_Cerebellum_White_Matter: limiting intensities to 88.0 --> 255.0 0 of 102 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (88, 116, 65) --> (129, 151, 115) Right_Cerebellum_White_Matter: limiting intensities to 95.0 --> 255.0 0 of 89 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 116, 94) --> (142, 167, 125) Brain_Stem: limiting intensities to 105.0 --> 255.0 45 of 97 (46.4%) samples deleted using 1145 total control points for intensity normalization... bias field = 0.978 +- 0.077 0 of 1099 control points discarded finding control points in Left_Cerebral_White_Matter.... found 41584 control points for structure... bounding box (127, 56, 50) --> (185, 151, 198) Left_Cerebral_White_Matter: limiting intensities to 92.0 --> 255.0 13 of 428 (3.0%) samples deleted finding control points in Right_Cerebral_White_Matter.... found 40735 control points for structure... bounding box (73, 55, 52) --> (129, 150, 198) Right_Cerebral_White_Matter: limiting intensities to 93.0 --> 122.0 8 of 503 (1.6%) samples deleted finding control points in Left_Cerebellum_White_Matter.... found 3012 control points for structure... bounding box (130, 116, 67) --> (170, 152, 115) Left_Cerebellum_White_Matter: limiting intensities to 84.0 --> 255.0 0 of 110 (0.0%) samples deleted finding control points in Right_Cerebellum_White_Matter.... found 2764 control points for structure... bounding box (88, 116, 65) --> (129, 151, 115) Right_Cerebellum_White_Matter: limiting intensities to 87.0 --> 255.0 0 of 98 (0.0%) samples deleted finding control points in Brain_Stem.... found 3520 control points for structure... bounding box (114, 116, 94) --> (142, 167, 125) Brain_Stem: limiting intensities to 98.0 --> 255.0 41 of 118 (34.7%) samples deleted using 1257 total control points for intensity normalization... bias field = 0.988 +- 0.057 0 of 1195 control points discarded writing normalized volume to norm.mgz... writing control points to ctrl_pts.mgz freeing GCA...done. normalization took 1 minutes and 43 seconds. #-------------------------------------- #@# CA Reg Fri Mar 18 12:58:17 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/mri mri_ca_register -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/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 '/neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/RB_all_2008-03-26.gca'... label assignment complete, 0 changed (0.00%) det(m_affine) = 1.73 (predicted orig area = 4.6) 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=0.821, neg=0, invalid=96777 0001: dt=129.472000, rms=0.779 (5.101%), neg=0, invalid=96777 0002: dt=129.472000, rms=0.767 (1.493%), neg=0, invalid=96777 0003: dt=129.472000, rms=0.758 (1.252%), neg=0, invalid=96777 0004: dt=55.488000, rms=0.756 (0.170%), neg=0, invalid=96777 0005: dt=55.488000, rms=0.755 (0.159%), neg=0, invalid=96777 0006: dt=55.488000, rms=0.752 (0.420%), neg=0, invalid=96777 0007: dt=55.488000, rms=0.746 (0.831%), neg=0, invalid=96777 0008: dt=55.488000, rms=0.741 (0.606%), neg=0, invalid=96777 0009: dt=55.488000, rms=0.738 (0.470%), neg=0, invalid=96777 0010: dt=55.488000, rms=0.734 (0.461%), neg=0, invalid=96777 0011: dt=55.488000, rms=0.734 (0.059%), neg=0, invalid=96777 0012: dt=55.488000, rms=0.733 (0.078%), neg=0, invalid=96777 0013: dt=55.488000, rms=0.733 (0.090%), neg=0, invalid=96777 0014: dt=55.488000, rms=0.731 (0.171%), neg=0, invalid=96777 0015: dt=55.488000, rms=0.729 (0.271%), neg=0, invalid=96777 0016: dt=55.488000, rms=0.728 (0.221%), neg=0, invalid=96777 0017: dt=55.488000, rms=0.727 (0.103%), neg=0, invalid=96777 0018: dt=55.488000, rms=0.726 (0.168%), neg=0, invalid=96777 0019: dt=55.488000, rms=0.725 (0.188%), neg=0, invalid=96777 0020: dt=55.488000, rms=0.723 (0.231%), neg=0, invalid=96777 0021: dt=55.488000, rms=0.721 (0.258%), neg=0, invalid=96777 0022: dt=55.488000, rms=0.719 (0.251%), neg=0, invalid=96777 0023: dt=55.488000, rms=0.718 (0.216%), neg=0, invalid=96777 0024: dt=55.488000, rms=0.717 (0.143%), neg=0, invalid=96777 0025: dt=55.488000, rms=0.717 (0.014%), neg=0, invalid=96777 0026: dt=55.488000, rms=0.716 (0.023%), neg=0, invalid=96777 0027: dt=55.488000, rms=0.716 (0.019%), neg=0, invalid=96777 0028: dt=443.904000, rms=0.715 (0.190%), neg=0, invalid=96777 0029: dt=92.480000, rms=0.715 (0.032%), neg=0, invalid=96777 0030: dt=92.480000, rms=0.715 (0.001%), neg=0, invalid=96777 0031: dt=92.480000, rms=0.714 (0.022%), neg=0, invalid=96777 0032: dt=92.480000, rms=0.714 (0.046%), neg=0, invalid=96777 0033: dt=92.480000, rms=0.714 (0.052%), neg=0, invalid=96777 0034: dt=92.480000, rms=0.713 (0.054%), neg=0, invalid=96777 0035: dt=92.480000, rms=0.713 (0.030%), neg=0, invalid=96777 0036: dt=92.480000, rms=0.713 (0.028%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.713, neg=0, invalid=96777 0037: dt=129.472000, rms=0.712 (0.199%), neg=0, invalid=96777 0038: dt=369.920000, rms=0.711 (0.087%), neg=0, invalid=96777 0039: dt=369.920000, rms=0.710 (0.074%), neg=0, invalid=96777 0040: dt=369.920000, rms=0.710 (-1.733%), neg=0, invalid=96777 setting smoothness coefficient to 0.154 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.714, neg=0, invalid=96777 0041: dt=36.288000, rms=0.711 (0.431%), neg=0, invalid=96777 0042: dt=145.152000, rms=0.704 (0.912%), neg=0, invalid=96777 0043: dt=20.736000, rms=0.702 (0.279%), neg=0, invalid=96777 0044: dt=414.720000, rms=0.686 (2.277%), neg=0, invalid=96777 0045: dt=31.104000, rms=0.681 (0.845%), neg=0, invalid=96777 0046: dt=20.736000, rms=0.680 (0.096%), neg=0, invalid=96777 0047: dt=20.736000, rms=0.680 (0.049%), neg=0, invalid=96777 0048: dt=20.736000, rms=0.679 (0.038%), neg=0, invalid=96777 0049: dt=20.736000, rms=0.679 (0.009%), neg=0, invalid=96777 0050: dt=248.832000, rms=0.674 (0.832%), neg=0, invalid=96777 0051: dt=25.920000, rms=0.673 (0.112%), neg=0, invalid=96777 0052: dt=25.920000, rms=0.673 (0.020%), neg=0, invalid=96777 0053: dt=25.920000, rms=0.673 (-0.004%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.673, neg=0, invalid=96777 0054: dt=82.944000, rms=0.670 (0.437%), neg=0, invalid=96777 0055: dt=124.416000, rms=0.667 (0.331%), neg=0, invalid=96777 0056: dt=36.288000, rms=0.666 (0.258%), neg=0, invalid=96777 0057: dt=36.288000, rms=0.666 (0.041%), neg=0, invalid=96777 0058: dt=36.288000, rms=0.665 (0.120%), neg=0, invalid=96777 0059: dt=36.288000, rms=0.664 (0.154%), neg=0, invalid=96777 0060: dt=36.288000, rms=0.663 (0.156%), neg=0, invalid=96777 0061: dt=36.288000, rms=0.661 (0.201%), neg=0, invalid=96777 0062: dt=36.288000, rms=0.660 (0.237%), neg=0, invalid=96777 0063: dt=36.288000, rms=0.658 (0.242%), neg=0, invalid=96777 0064: dt=36.288000, rms=0.657 (0.208%), neg=0, invalid=96777 0065: dt=36.288000, rms=0.655 (0.195%), neg=0, invalid=96777 0066: dt=36.288000, rms=0.654 (0.258%), neg=0, invalid=96777 0067: dt=36.288000, rms=0.652 (0.298%), neg=0, invalid=96777 0068: dt=36.288000, rms=0.650 (0.265%), neg=0, invalid=96777 0069: dt=36.288000, rms=0.648 (0.249%), neg=0, invalid=96777 0070: dt=36.288000, rms=0.647 (0.267%), neg=0, invalid=96777 0071: dt=36.288000, rms=0.645 (0.251%), neg=0, invalid=96777 0072: dt=36.288000, rms=0.644 (0.219%), neg=0, invalid=96777 0073: dt=36.288000, rms=0.643 (0.187%), neg=0, invalid=96777 0074: dt=36.288000, rms=0.641 (0.214%), neg=0, invalid=96777 0075: dt=36.288000, rms=0.640 (0.217%), neg=0, invalid=96777 0076: dt=36.288000, rms=0.639 (0.162%), neg=0, invalid=96777 0077: dt=36.288000, rms=0.638 (0.127%), neg=0, invalid=96777 0078: dt=36.288000, rms=0.637 (0.137%), neg=0, invalid=96777 0079: dt=36.288000, rms=0.636 (0.155%), neg=0, invalid=96777 0080: dt=36.288000, rms=0.635 (0.141%), neg=0, invalid=96777 0081: dt=36.288000, rms=0.634 (0.121%), neg=0, invalid=96777 0082: dt=36.288000, rms=0.634 (0.110%), neg=0, invalid=96777 0083: dt=62.208000, rms=0.633 (0.052%), neg=0, invalid=96777 0084: dt=62.208000, rms=0.633 (-0.073%), neg=0, invalid=96777 setting smoothness coefficient to 0.588 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.652, neg=0, invalid=96777 0085: dt=0.000000, rms=0.652 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.652, neg=0, invalid=96777 0086: dt=0.000000, rms=0.652 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.709, neg=0, invalid=96777 0087: dt=3.456000, rms=0.697 (1.659%), neg=0, invalid=96777 0088: dt=0.944444, rms=0.697 (0.030%), neg=0, invalid=96777 0089: dt=0.944444, rms=0.697 (-0.015%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.697, neg=0, invalid=96777 0090: dt=3.456000, rms=0.695 (0.333%), neg=0, invalid=96777 0091: dt=0.432000, rms=0.695 (0.006%), neg=0, invalid=96777 0092: dt=0.432000, rms=0.695 (-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=0.747, neg=0, invalid=96777 0093: dt=0.866873, rms=0.746 (0.147%), neg=0, invalid=96777 0094: dt=1.413793, rms=0.744 (0.287%), neg=0, invalid=96777 0095: dt=0.448000, rms=0.744 (0.014%), neg=0, invalid=96777 0096: dt=0.448000, rms=0.744 (0.003%), neg=0, invalid=96777 0097: dt=0.448000, rms=0.744 (-0.012%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.744, neg=0, invalid=96777 0098: dt=3.196262, rms=0.729 (1.980%), neg=0, invalid=96777 0099: dt=0.000000, rms=0.729 (0.001%), neg=0, invalid=96777 0100: dt=0.100000, rms=0.729 (-0.057%), 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=0.688, neg=0, invalid=96777 0101: dt=0.448000, rms=0.646 (6.144%), neg=0, invalid=96777 0102: dt=0.000000, rms=0.646 (0.004%), neg=0, invalid=96777 0103: dt=0.050000, rms=0.646 (-1.972%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.646, neg=0, invalid=96777 0104: dt=0.000000, rms=0.646 (0.000%), neg=0, invalid=96777 renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.11725 (24) mri peak = 0.21224 (12) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (800 voxels, overlap=0.003) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (800 voxels, peak = 9), gca=9.6 gca peak = 0.14022 (22) mri peak = 0.05131 (14) Right_Lateral_Ventricle (43): linear fit = 0.62 x + 0.0 (459 voxels, overlap=0.230) Right_Lateral_Ventricle (43): linear fit = 0.62 x + 0.0 (459 voxels, peak = 14), gca=13.8 gca peak = 0.24234 (100) mri peak = 0.10526 (85) Right_Pallidum (52): linear fit = 0.89 x + 0.0 (284 voxels, overlap=0.099) Right_Pallidum (52): linear fit = 0.89 x + 0.0 (284 voxels, peak = 90), gca=89.5 gca peak = 0.19192 (97) mri peak = 0.21732 (84) Left_Pallidum (13): linear fit = 0.88 x + 0.0 (225 voxels, overlap=0.225) Left_Pallidum (13): linear fit = 0.88 x + 0.0 (225 voxels, peak = 85), gca=84.9 gca peak = 0.24007 (63) mri peak = 0.21170 (76) Right_Hippocampus (53): linear fit = 1.20 x + 0.0 (602 voxels, overlap=0.022) Right_Hippocampus (53): linear fit = 1.20 x + 0.0 (602 voxels, peak = 75), gca=75.3 gca peak = 0.29892 (64) mri peak = 0.13947 (75) Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (546 voxels, overlap=0.076) Left_Hippocampus (17): linear fit = 1.13 x + 0.0 (546 voxels, peak = 73), gca=72.6 gca peak = 0.12541 (104) mri peak = 0.08905 (109) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (41047 voxels, overlap=0.621) Right_Cerebral_White_Matter (41): linear fit = 1.05 x + 0.0 (41047 voxels, peak = 110), gca=109.7 gca peak = 0.13686 (104) mri peak = 0.08684 (110) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (43183 voxels, overlap=0.651) Left_Cerebral_White_Matter (2): linear fit = 1.04 x + 0.0 (43183 voxels, peak = 109), gca=108.7 gca peak = 0.11691 (63) mri peak = 0.04984 (70) Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (21979 voxels, overlap=0.814) Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (21979 voxels, peak = 70), gca=70.2 gca peak = 0.13270 (63) mri peak = 0.06096 (70) Right_Cerebral_Cortex (42): linear fit = 1.09 x + 0.0 (23933 voxels, overlap=0.730) Right_Cerebral_Cortex (42): linear fit = 1.09 x + 0.0 (23933 voxels, peak = 68), gca=68.4 gca peak = 0.15182 (70) mri peak = 0.19266 (82) Right_Caudate (50): linear fit = 1.11 x + 0.0 (225 voxels, overlap=0.114) Right_Caudate (50): linear fit = 1.11 x + 0.0 (225 voxels, peak = 77), gca=77.3 gca peak = 0.14251 (76) mri peak = 0.10787 (82) Left_Caudate (11): linear fit = 1.05 x + 0.0 (495 voxels, overlap=0.617) Left_Caudate (11): linear fit = 1.05 x + 0.0 (495 voxels, peak = 80), gca=80.2 gca peak = 0.12116 (60) mri peak = 0.05261 (72) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (19778 voxels, overlap=0.712) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (19778 voxels, peak = 68), gca=67.5 gca peak = 0.12723 (61) mri peak = 0.05070 (69) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (23154 voxels, overlap=0.511) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (23154 voxels, peak = 70), gca=70.5 gca peak = 0.22684 (88) mri peak = 0.05183 (95) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (6444 voxels, overlap=0.583) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (6444 voxels, peak = 95), gca=95.5 gca peak = 0.21067 (87) mri peak = 0.08201 (92) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5634 voxels, overlap=0.386) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5634 voxels, peak = 94), gca=93.5 gca peak = 0.25455 (62) mri peak = 0.14645 (71) Left_Amygdala (18): linear fit = 1.13 x + 0.0 (251 voxels, overlap=0.072) Left_Amygdala (18): linear fit = 1.13 x + 0.0 (251 voxels, peak = 70), gca=70.4 gca peak = 0.39668 (62) mri peak = 0.35700 (73) Right_Amygdala (54): linear fit = 1.16 x + 0.0 (242 voxels, overlap=0.010) Right_Amygdala (54): linear fit = 1.16 x + 0.0 (242 voxels, peak = 72), gca=72.2 gca peak = 0.10129 (93) mri peak = 0.05920 (102) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (3662 voxels, overlap=0.425) Left_Thalamus_Proper (10): linear fit = 1.12 x + 0.0 (3662 voxels, peak = 105), gca=104.6 gca peak = 0.12071 (89) mri peak = 0.06081 (99) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (2729 voxels, overlap=0.440) Right_Thalamus_Proper (49): linear fit = 1.10 x + 0.0 (2729 voxels, peak = 97), gca=97.5 gca peak = 0.13716 (82) mri peak = 0.10553 (89) Left_Putamen (12): linear fit = 1.03 x + 0.0 (1788 voxels, overlap=0.779) Left_Putamen (12): linear fit = 1.03 x + 0.0 (1788 voxels, peak = 85), gca=84.9 gca peak = 0.15214 (84) mri peak = 0.11695 (84) Right_Putamen (51): linear fit = 1.02 x + 0.0 (1693 voxels, overlap=0.984) Right_Putamen (51): linear fit = 1.02 x + 0.0 (1693 voxels, peak = 86), gca=86.1 gca peak = 0.08983 (85) mri peak = 0.06750 (103) Brain_Stem (16): linear fit = 1.18 x + 0.0 (7434 voxels, overlap=0.210) Brain_Stem (16): linear fit = 1.18 x + 0.0 (7434 voxels, peak = 101), gca=100.7 gca peak = 0.11809 (92) mri peak = 0.12040 (99) Right_VentralDC (60): linear fit = 1.13 x + 0.0 (404 voxels, overlap=0.448) Right_VentralDC (60): linear fit = 1.13 x + 0.0 (404 voxels, peak = 104), gca=104.4 gca peak = 0.12914 (94) mri peak = 0.09901 (97) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (518 voxels, overlap=0.366) Left_VentralDC (28): linear fit = 1.09 x + 0.0 (518 voxels, peak = 102), gca=102.0 gca peak = 0.21100 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.13542 (27) mri peak = 0.22049 (14) Fourth_Ventricle (15): linear fit = 0.49 x + 0.0 (238 voxels, overlap=0.020) Fourth_Ventricle (15): linear fit = 0.49 x + 0.0 (238 voxels, peak = 13), gca=13.1 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.21802 (40) gca peak Third_Ventricle = 0.21100 (36) 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 1.14 x + 0.0 estimating mean wm scale to be 1.05 x + 0.0 estimating mean csf scale to be 0.51 x + 0.0 saving intensity scales to talairach.label_intensities.txt **************** pass 1 of 1 ************************ setting smoothness coefficient to 0.008 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.676, neg=0, invalid=96777 0105: dt=23.120000, rms=0.674 (0.264%), neg=0, invalid=96777 0106: dt=8.092000, rms=0.674 (0.025%), neg=0, invalid=96777 0107: dt=8.092000, rms=0.674 (0.006%), neg=0, invalid=96777 0108: dt=8.092000, rms=0.674 (-0.030%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.674, neg=0, invalid=96777 0109: dt=32.368000, rms=0.671 (0.329%), neg=0, invalid=96777 0110: dt=32.368000, rms=0.670 (0.186%), neg=0, invalid=96777 0111: dt=32.368000, rms=0.669 (0.139%), neg=0, invalid=96777 0112: dt=8.092000, rms=0.669 (0.035%), neg=0, invalid=96777 0113: dt=8.092000, rms=0.669 (0.033%), neg=0, invalid=96777 0114: dt=1.011500, rms=0.669 (0.003%), neg=0, invalid=96777 0115: dt=0.126438, rms=0.669 (0.001%), neg=0, invalid=96777 0116: dt=0.090789, rms=0.669 (0.000%), neg=0, invalid=96777 0117: dt=0.005674, rms=0.669 (0.000%), neg=0, invalid=96777 0118: dt=0.000709, rms=0.669 (0.000%), neg=0, invalid=96777 0119: dt=0.000355, rms=0.669 (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=0.669, neg=0, invalid=96777 0120: dt=0.000000, rms=0.669 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.669, neg=0, invalid=96777 0121: dt=0.000000, rms=0.669 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.669, neg=0, invalid=96777 0122: dt=11.200000, rms=0.643 (3.824%), neg=0, invalid=96777 0123: dt=38.400000, rms=0.612 (4.846%), neg=0, invalid=96777 0124: dt=0.700000, rms=0.612 (0.067%), neg=0, invalid=96777 0125: dt=0.043750, rms=0.612 (0.009%), neg=0, invalid=96777 0126: dt=0.043750, rms=0.612 (0.005%), neg=0, invalid=96777 0127: dt=0.005469, rms=0.612 (0.001%), neg=0, invalid=96777 0128: dt=0.002734, rms=0.612 (0.000%), neg=0, invalid=96777 0129: dt=0.002344, rms=0.612 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.612, neg=0, invalid=96777 0130: dt=0.000000, rms=0.612 (0.000%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.615, neg=0, invalid=96777 0131: dt=0.000246, rms=0.615 (0.000%), neg=0, invalid=96777 0132: dt=0.000000, rms=0.615 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.615, neg=0, invalid=96777 0133: dt=0.000000, rms=0.615 (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=0.623, neg=0, invalid=96777 0134: dt=0.448000, rms=0.616 (1.080%), neg=0, invalid=96777 0135: dt=0.448000, rms=0.611 (0.895%), neg=0, invalid=96777 0136: dt=0.448000, rms=0.606 (0.715%), neg=0, invalid=96777 0137: dt=0.448000, rms=0.603 (0.552%), neg=0, invalid=96777 0138: dt=0.448000, rms=0.600 (0.449%), neg=0, invalid=96777 0139: dt=0.448000, rms=0.598 (0.366%), neg=0, invalid=96777 0140: dt=0.448000, rms=0.596 (0.298%), neg=0, invalid=96777 0141: dt=1.536000, rms=0.591 (0.813%), neg=0, invalid=96777 0142: dt=1.280000, rms=0.590 (0.276%), neg=0, invalid=96777 0143: dt=1.792000, rms=0.588 (0.207%), neg=0, invalid=96777 0144: dt=1.792000, rms=0.588 (0.068%), neg=0, invalid=96777 0145: dt=0.448000, rms=0.588 (0.007%), neg=0, invalid=96777 0146: dt=0.448000, rms=0.588 (0.003%), neg=0, invalid=96777 0147: dt=0.448000, rms=0.588 (0.003%), neg=0, invalid=96777 0148: dt=0.448000, rms=0.588 (-0.003%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.588, neg=0, invalid=96777 0149: dt=1.792000, rms=0.580 (1.367%), neg=0, invalid=96777 0150: dt=1.792000, rms=0.577 (0.565%), neg=0, invalid=96777 0151: dt=1.792000, rms=0.575 (0.298%), neg=0, invalid=96777 0152: dt=1.792000, rms=0.574 (0.155%), neg=0, invalid=96777 0153: dt=1.792000, rms=0.573 (0.105%), neg=0, invalid=96777 0154: dt=1.792000, rms=0.573 (0.063%), neg=0, invalid=96777 0155: dt=1.792000, rms=0.573 (0.058%), neg=0, invalid=96777 0156: dt=1.536000, rms=0.573 (0.040%), neg=0, invalid=96777 0157: dt=0.768000, rms=0.572 (0.017%), neg=0, invalid=96777 0158: dt=0.768000, rms=0.572 (0.013%), neg=0, invalid=96777 0159: dt=0.768000, rms=0.572 (0.020%), neg=0, invalid=96777 0160: dt=0.768000, rms=0.572 (0.021%), neg=0, invalid=96777 0161: dt=0.768000, rms=0.572 (0.019%), neg=0, invalid=96777 0162: dt=0.448000, rms=0.572 (0.003%), 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=0.563, neg=0, invalid=96777 0163: dt=0.112000, rms=0.556 (1.221%), neg=0, invalid=96777 0164: dt=0.112000, rms=0.551 (0.859%), neg=0, invalid=96777 0165: dt=0.007000, rms=0.551 (0.040%), neg=0, invalid=96777 0166: dt=0.007000, rms=0.550 (0.040%), neg=0, invalid=96777 0167: dt=0.007000, rms=0.550 (0.075%), neg=0, invalid=96777 0168: dt=0.007000, rms=0.550 (0.105%), neg=0, invalid=96777 0169: dt=0.007000, rms=0.549 (0.129%), neg=0, invalid=96777 0170: dt=0.007000, rms=0.548 (0.153%), neg=0, invalid=96777 0171: dt=0.007000, rms=0.547 (0.171%), neg=0, invalid=96777 0172: dt=0.007000, rms=0.546 (0.183%), neg=0, invalid=96777 0173: dt=0.007000, rms=0.545 (0.190%), neg=0, invalid=96777 0174: dt=0.007000, rms=0.544 (0.194%), neg=0, invalid=96777 0175: dt=0.007000, rms=0.543 (0.196%), neg=0, invalid=96777 0176: dt=0.007000, rms=0.542 (0.197%), neg=0, invalid=96777 0177: dt=0.007000, rms=0.541 (0.194%), neg=0, invalid=96777 0178: dt=0.007000, rms=0.540 (0.187%), neg=0, invalid=96777 0179: dt=0.007000, rms=0.539 (0.181%), neg=0, invalid=96777 0180: dt=0.007000, rms=0.538 (0.172%), neg=0, invalid=96777 0181: dt=0.007000, rms=0.537 (0.164%), neg=0, invalid=96777 0182: dt=0.007000, rms=0.536 (0.155%), neg=0, invalid=96777 0183: dt=0.007000, rms=0.535 (0.140%), neg=0, invalid=96777 0184: dt=0.007000, rms=0.535 (0.133%), neg=0, invalid=96777 0185: dt=0.007000, rms=0.534 (0.119%), neg=0, invalid=96777 0186: dt=0.007000, rms=0.533 (0.110%), neg=0, invalid=96777 0187: dt=0.007000, rms=0.533 (0.099%), neg=0, invalid=96777 0188: dt=0.007000, rms=0.532 (0.089%), neg=0, invalid=96777 0189: dt=0.007000, rms=0.532 (0.080%), neg=0, invalid=96777 0190: dt=0.007000, rms=0.532 (0.072%), neg=0, invalid=96777 0191: dt=0.007000, rms=0.531 (0.063%), neg=0, invalid=96777 0192: dt=0.007000, rms=0.531 (0.055%), neg=0, invalid=96777 0193: dt=0.007000, rms=0.531 (0.050%), neg=0, invalid=96777 0194: dt=0.007000, rms=0.531 (0.042%), neg=0, invalid=96777 0195: dt=0.007000, rms=0.530 (0.037%), neg=0, invalid=96777 0196: dt=0.007000, rms=0.530 (0.032%), neg=0, invalid=96777 0197: dt=0.007000, rms=0.530 (0.029%), neg=0, invalid=96777 0198: dt=0.007000, rms=0.530 (0.025%), neg=0, invalid=96777 0199: dt=0.007000, rms=0.530 (0.022%), neg=0, invalid=96777 0200: dt=0.007000, rms=0.530 (0.021%), neg=0, invalid=96777 0201: dt=0.028000, rms=0.530 (0.005%), neg=0, invalid=96777 0202: dt=0.028000, rms=0.530 (0.004%), neg=0, invalid=96777 0203: dt=0.028000, rms=0.530 (0.009%), neg=0, invalid=96777 0204: dt=0.028000, rms=0.529 (0.012%), neg=0, invalid=96777 0205: dt=0.028000, rms=0.529 (0.013%), neg=0, invalid=96777 0206: dt=0.028000, rms=0.529 (0.020%), neg=0, invalid=96777 0207: dt=0.028000, rms=0.529 (0.024%), neg=0, invalid=96777 0208: dt=0.028000, rms=0.529 (0.025%), neg=0, invalid=96777 0209: dt=0.028000, rms=0.529 (0.032%), neg=0, invalid=96777 0210: dt=0.028000, rms=0.529 (0.036%), neg=0, invalid=96777 0211: dt=0.028000, rms=0.528 (0.043%), neg=0, invalid=96777 0212: dt=0.028000, rms=0.528 (0.043%), neg=0, invalid=96777 0213: dt=0.028000, rms=0.528 (0.049%), neg=0, invalid=96777 0214: dt=0.028000, rms=0.528 (0.052%), neg=0, invalid=96777 0215: dt=0.028000, rms=0.527 (0.054%), neg=0, invalid=96777 0216: dt=0.028000, rms=0.527 (0.056%), neg=0, invalid=96777 0217: dt=0.028000, rms=0.527 (0.057%), neg=0, invalid=96777 0218: dt=0.028000, rms=0.526 (0.059%), neg=0, invalid=96777 0219: dt=0.028000, rms=0.526 (0.059%), neg=0, invalid=96777 0220: dt=0.028000, rms=0.526 (0.059%), neg=0, invalid=96777 0221: dt=0.028000, rms=0.526 (0.054%), neg=0, invalid=96777 0222: dt=0.028000, rms=0.525 (0.047%), neg=0, invalid=96777 0223: dt=0.001750, rms=0.525 (0.002%), neg=0, invalid=96777 0224: dt=0.001750, rms=0.525 (-0.000%), neg=0, invalid=96777 0225: dt=0.028000, rms=0.525 (0.002%), neg=0, invalid=96777 0226: dt=0.112000, rms=0.525 (0.006%), neg=0, invalid=96777 0227: dt=0.028000, 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 0228: dt=0.115702, rms=0.523 (0.367%), neg=0, invalid=96777 0229: dt=0.096000, rms=0.522 (0.221%), neg=0, invalid=96777 0230: dt=0.001750, rms=0.522 (0.001%), neg=0, invalid=96777 0231: dt=0.001750, rms=0.522 (0.003%), neg=0, invalid=96777 0232: dt=0.001750, rms=0.522 (0.006%), neg=0, invalid=96777 0233: dt=0.001750, rms=0.522 (0.009%), neg=0, invalid=96777 0234: dt=0.001750, rms=0.522 (0.011%), neg=0, invalid=96777 0235: dt=0.001750, rms=0.522 (0.012%), neg=0, invalid=96777 0236: dt=0.001750, rms=0.522 (0.016%), neg=0, invalid=96777 0237: dt=0.001750, rms=0.522 (0.015%), neg=0, invalid=96777 0238: dt=0.001750, rms=0.522 (0.015%), neg=0, invalid=96777 0239: dt=0.001750, rms=0.522 (0.018%), neg=0, invalid=96777 0240: dt=0.001750, rms=0.522 (0.017%), neg=0, invalid=96777 0241: dt=0.080000, rms=0.521 (0.116%), neg=0, invalid=96777 0242: dt=0.001750, rms=0.521 (0.002%), neg=0, invalid=96777 0243: dt=0.001750, rms=0.521 (0.002%), neg=0, invalid=96777 0244: dt=0.001750, rms=0.521 (0.004%), neg=0, invalid=96777 0245: dt=0.001750, rms=0.521 (0.006%), neg=0, invalid=96777 0246: dt=0.001750, rms=0.521 (0.009%), neg=0, invalid=96777 0247: dt=0.001750, rms=0.521 (0.009%), neg=0, invalid=96777 0248: dt=0.001750, rms=0.521 (0.009%), neg=0, invalid=96777 0249: dt=0.001750, rms=0.521 (0.010%), neg=0, invalid=96777 0250: dt=0.001750, rms=0.521 (0.010%), neg=0, invalid=96777 0251: dt=0.001750, rms=0.521 (0.012%), neg=0, invalid=96777 0252: dt=0.001750, rms=0.521 (0.012%), neg=0, invalid=96777 0253: dt=0.090572, rms=0.520 (0.089%), neg=0, invalid=96777 0254: dt=0.001750, rms=0.520 (-0.001%), neg=0, invalid=96777 0255: dt=0.001750, rms=0.520 (0.001%), neg=0, invalid=96777 0256: dt=0.001750, rms=0.520 (0.004%), neg=0, invalid=96777 0257: dt=0.001750, rms=0.520 (0.002%), neg=0, invalid=96777 0258: dt=0.001750, rms=0.520 (0.003%), neg=0, invalid=96777 0259: dt=0.001750, rms=0.520 (0.004%), neg=0, invalid=96777 0260: dt=0.001750, rms=0.520 (0.005%), neg=0, invalid=96777 0261: dt=0.001750, rms=0.520 (0.004%), 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=0.517, neg=0, invalid=96777 0262: dt=0.000000, rms=0.517 (0.000%), neg=0, invalid=96777 0263: dt=0.000000, rms=0.517 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.517, neg=0, invalid=96777 0264: dt=32.368000, rms=0.517 (0.057%), neg=0, invalid=96777 0265: dt=0.000000, rms=0.517 (0.002%), neg=0, invalid=96777 0266: dt=0.850000, rms=0.517 (-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=0.517, neg=0, invalid=96777 0267: dt=0.141750, rms=0.517 (0.000%), neg=0, invalid=96777 0268: dt=0.141750, rms=0.517 (0.000%), neg=0, invalid=96777 0269: dt=0.006328, rms=0.517 (0.000%), neg=0, invalid=96777 0270: dt=0.006328, rms=0.517 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.517, neg=0, invalid=96777 0271: dt=36.288000, rms=0.515 (0.297%), neg=0, invalid=96777 0272: dt=124.416000, rms=0.512 (0.538%), neg=0, invalid=96777 0273: dt=15.552000, rms=0.512 (0.086%), neg=0, invalid=96777 0274: dt=15.552000, rms=0.511 (0.082%), neg=0, invalid=96777 0275: dt=15.552000, rms=0.511 (0.132%), neg=0, invalid=96777 0276: dt=15.552000, rms=0.510 (0.163%), neg=0, invalid=96777 0277: dt=15.552000, rms=0.509 (0.178%), neg=0, invalid=96777 0278: dt=15.552000, rms=0.508 (0.169%), neg=0, invalid=96777 0279: dt=15.552000, rms=0.507 (0.158%), neg=0, invalid=96777 0280: dt=15.552000, rms=0.507 (0.139%), neg=0, invalid=96777 0281: dt=15.552000, rms=0.506 (0.119%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0282: dt=15.552000, rms=0.506 (0.097%), neg=0, invalid=96777 0283: dt=145.152000, rms=0.505 (0.107%), neg=0, invalid=96777 0284: dt=25.920000, rms=0.504 (0.130%), neg=0, invalid=96777 0285: dt=20.736000, rms=0.504 (0.016%), neg=0, invalid=96777 0286: dt=20.736000, rms=0.504 (0.029%), neg=0, invalid=96777 0287: dt=20.736000, rms=0.504 (0.047%), neg=0, invalid=96777 0288: dt=20.736000, rms=0.504 (0.059%), neg=0, invalid=96777 0289: dt=20.736000, rms=0.503 (0.065%), neg=0, invalid=96777 0290: dt=20.736000, rms=0.503 (0.075%), neg=0, invalid=96777 0291: dt=20.736000, rms=0.502 (0.086%), neg=0, invalid=96777 0292: dt=20.736000, rms=0.502 (0.089%), neg=0, invalid=96777 0293: dt=20.736000, rms=0.502 (0.089%), neg=0, invalid=96777 0294: dt=20.736000, rms=0.501 (0.085%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.502, neg=0, invalid=96777 0295: dt=3.555556, rms=0.502 (0.044%), neg=0, invalid=96777 0296: dt=2.800000, rms=0.502 (0.016%), neg=0, invalid=96777 0297: dt=2.800000, rms=0.502 (0.007%), neg=0, invalid=96777 0298: dt=2.800000, rms=0.502 (-0.026%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.502, neg=0, invalid=96777 iter 0, gcam->neg = 3 after 9 iterations, nbhd size=1, neg = 0 0299: dt=38.400000, rms=0.493 (1.635%), neg=0, invalid=96777 0300: dt=9.600000, rms=0.491 (0.532%), neg=0, invalid=96777 iter 0, gcam->neg = 17 after 10 iterations, nbhd size=1, neg = 0 0301: dt=44.800000, rms=0.488 (0.557%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0302: dt=14.651685, rms=0.486 (0.470%), neg=0, invalid=96777 0303: dt=11.200000, rms=0.485 (0.169%), neg=0, invalid=96777 0304: dt=11.200000, rms=0.484 (0.186%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0305: dt=11.200000, rms=0.483 (0.288%), neg=0, invalid=96777 0306: dt=11.200000, rms=0.481 (0.361%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0307: dt=11.200000, rms=0.479 (0.407%), neg=0, invalid=96777 0308: dt=11.200000, rms=0.477 (0.437%), neg=0, invalid=96777 0309: dt=11.200000, rms=0.475 (0.393%), neg=0, invalid=96777 0310: dt=11.200000, rms=0.473 (0.346%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 14 iterations, nbhd size=2, neg = 0 0311: dt=11.200000, rms=0.472 (0.357%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 13 iterations, nbhd size=2, neg = 0 0312: dt=11.200000, rms=0.470 (0.354%), neg=0, invalid=96777 0313: dt=11.200000, rms=0.468 (0.335%), neg=0, invalid=96777 0314: dt=11.200000, rms=0.467 (0.273%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0315: dt=11.200000, rms=0.466 (0.244%), neg=0, invalid=96777 iter 0, gcam->neg = 3 after 6 iterations, nbhd size=1, neg = 0 0316: dt=11.200000, rms=0.465 (0.195%), neg=0, invalid=96777 0317: dt=11.200000, rms=0.464 (0.185%), neg=0, invalid=96777 0318: dt=11.200000, rms=0.464 (0.118%), neg=0, invalid=96777 0319: dt=11.200000, rms=0.463 (0.135%), neg=0, invalid=96777 0320: dt=11.200000, rms=0.463 (0.103%), neg=0, invalid=96777 0321: dt=11.200000, rms=0.462 (0.126%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0322: dt=11.200000, rms=0.462 (0.102%), neg=0, invalid=96777 0323: dt=11.200000, rms=0.461 (0.115%), neg=0, invalid=96777 0324: dt=11.200000, rms=0.461 (0.077%), neg=0, invalid=96777 0325: dt=8.000000, rms=0.461 (0.012%), neg=0, invalid=96777 0326: dt=8.000000, rms=0.461 (0.016%), neg=0, invalid=96777 0327: dt=8.000000, rms=0.461 (0.012%), neg=0, invalid=96777 0328: dt=8.000000, rms=0.460 (0.021%), neg=0, invalid=96777 0329: dt=8.000000, rms=0.460 (0.009%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.470, neg=0, invalid=96777 0330: dt=0.000000, rms=0.470 (0.000%), neg=0, invalid=96777 0331: dt=0.000000, rms=0.470 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.470, neg=0, invalid=96777 0332: dt=1.008000, rms=0.470 (0.011%), neg=0, invalid=96777 0333: dt=1.008000, rms=0.470 (0.004%), neg=0, invalid=96777 0334: dt=1.008000, rms=0.470 (0.002%), neg=0, invalid=96777 0335: dt=1.008000, rms=0.470 (-0.028%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.489, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 5 iterations, nbhd size=1, neg = 0 0336: dt=0.573529, rms=0.488 (0.142%), neg=0, invalid=96777 0337: dt=0.320000, rms=0.488 (0.018%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0338: dt=0.320000, rms=0.488 (-0.017%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.488, neg=0, invalid=96777 iter 0, gcam->neg = 16 after 8 iterations, nbhd size=1, neg = 0 0339: dt=1.034749, rms=0.487 (0.294%), neg=0, invalid=96777 0340: dt=0.842105, rms=0.486 (0.066%), neg=0, invalid=96777 0341: dt=0.842105, rms=0.486 (-0.010%), 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=0.467, neg=0, invalid=96777 iter 0, gcam->neg = 471 after 10 iterations, nbhd size=1, neg = 0 0342: dt=1.109253, rms=0.443 (5.102%), neg=0, invalid=96777 0343: dt=0.000438, rms=0.443 (-0.009%), neg=0, invalid=96777 0344: dt=0.000438, rms=0.443 (0.001%), neg=0, invalid=96777 0345: dt=0.000438, rms=0.443 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.443, neg=0, invalid=96777 iter 0, gcam->neg = 1 after 1 iterations, nbhd size=0, neg = 0 0346: dt=0.020000, rms=0.443 (0.034%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0347: dt=0.112000, rms=0.442 (0.132%), neg=0, invalid=96777 0348: dt=0.000000, rms=0.442 (0.006%), neg=0, invalid=96777 iter 0, gcam->neg = 33 after 6 iterations, nbhd size=1, neg = 0 0349: dt=0.050000, rms=0.442 (-0.041%), 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=0.439, neg=0, invalid=96777 0350: dt=0.000000, rms=0.439 (-0.114%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.439, neg=0, invalid=96777 0351: dt=73.984000, rms=0.439 (0.065%), neg=0, invalid=96777 0352: dt=8.092000, rms=0.439 (0.003%), neg=0, invalid=96777 0353: dt=8.092000, rms=0.439 (0.000%), neg=0, invalid=96777 0354: dt=8.092000, rms=0.439 (-0.003%), neg=0, invalid=96777 setting smoothness coefficient to 0.031 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.439, neg=0, invalid=96777 0355: dt=0.000000, rms=0.439 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.439, neg=0, invalid=96777 0356: dt=25.920000, rms=0.439 (0.025%), neg=0, invalid=96777 0357: dt=82.944000, rms=0.438 (0.073%), neg=0, invalid=96777 0358: dt=31.104000, rms=0.438 (0.018%), neg=0, invalid=96777 0359: dt=31.104000, rms=0.438 (0.024%), neg=0, invalid=96777 0360: dt=31.104000, rms=0.438 (0.036%), neg=0, invalid=96777 0361: dt=31.104000, rms=0.438 (0.040%), neg=0, invalid=96777 0362: dt=31.104000, rms=0.438 (0.016%), neg=0, invalid=96777 0363: dt=31.104000, rms=0.438 (0.007%), neg=0, invalid=96777 setting smoothness coefficient to 0.118 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.438, neg=0, invalid=96777 0364: dt=2.000000, rms=0.438 (0.008%), neg=0, invalid=96777 0365: dt=0.400000, rms=0.438 (0.000%), neg=0, invalid=96777 0366: dt=0.400000, rms=0.438 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.438, neg=0, invalid=96777 iter 0, gcam->neg = 21 after 26 iterations, nbhd size=3, neg = 0 0367: dt=44.800000, rms=0.434 (0.899%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0368: dt=8.000000, rms=0.433 (0.224%), neg=0, invalid=96777 0369: dt=8.000000, rms=0.433 (0.114%), neg=0, invalid=96777 0370: dt=8.000000, rms=0.432 (0.139%), neg=0, invalid=96777 iter 0, gcam->neg = 2 after 12 iterations, nbhd size=2, neg = 0 0371: dt=8.000000, rms=0.431 (0.164%), neg=0, invalid=96777 0372: dt=8.000000, rms=0.430 (0.231%), neg=0, invalid=96777 0373: dt=8.000000, rms=0.429 (0.256%), neg=0, invalid=96777 iter 0, gcam->neg = 1 after 0 iterations, nbhd size=0, neg = 0 0374: dt=8.000000, rms=0.428 (0.249%), neg=0, invalid=96777 0375: dt=8.000000, rms=0.427 (0.240%), neg=0, invalid=96777 0376: dt=8.000000, rms=0.426 (0.199%), neg=0, invalid=96777 0377: dt=8.000000, rms=0.425 (0.164%), neg=0, invalid=96777 0378: dt=8.000000, rms=0.425 (0.152%), neg=0, invalid=96777 0379: dt=8.000000, rms=0.424 (0.153%), neg=0, invalid=96777 0380: dt=8.000000, rms=0.424 (0.125%), neg=0, invalid=96777 0381: dt=8.000000, rms=0.423 (0.120%), neg=0, invalid=96777 0382: dt=19.200000, rms=0.423 (0.074%), neg=0, invalid=96777 0383: dt=19.200000, rms=0.423 (0.041%), neg=0, invalid=96777 0384: dt=19.200000, rms=0.422 (0.054%), neg=0, invalid=96777 0385: dt=19.200000, rms=0.422 (-0.004%), neg=0, invalid=96777 setting smoothness coefficient to 0.400 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.426, neg=0, invalid=96777 0386: dt=0.180000, rms=0.426 (0.002%), neg=0, invalid=96777 0387: dt=1.008000, rms=0.426 (0.024%), neg=0, invalid=96777 0388: dt=1.008000, rms=0.426 (0.009%), neg=0, invalid=96777 0389: dt=1.008000, rms=0.426 (-0.002%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.426, neg=0, invalid=96777 iter 0, gcam->neg = 46 after 28 iterations, nbhd size=3, neg = 0 0390: dt=11.911111, rms=0.423 (0.534%), neg=0, invalid=96777 0391: dt=0.252000, rms=0.423 (0.014%), neg=0, invalid=96777 0392: dt=0.252000, rms=0.423 (0.014%), neg=0, invalid=96777 0393: dt=0.252000, rms=0.423 (0.026%), neg=0, invalid=96777 0394: dt=0.252000, rms=0.423 (0.035%), neg=0, invalid=96777 0395: dt=0.252000, rms=0.423 (0.041%), neg=0, invalid=96777 0396: dt=0.252000, rms=0.423 (0.044%), neg=0, invalid=96777 0397: dt=0.252000, rms=0.422 (0.045%), neg=0, invalid=96777 0398: dt=0.252000, rms=0.422 (0.045%), neg=0, invalid=96777 0399: dt=0.252000, rms=0.422 (0.044%), neg=0, invalid=96777 0400: dt=0.252000, rms=0.422 (0.044%), neg=0, invalid=96777 iter 0, gcam->neg = 14 after 23 iterations, nbhd size=3, neg = 0 0401: dt=11.520000, rms=0.421 (0.176%), neg=0, invalid=96777 0402: dt=0.533333, rms=0.421 (0.013%), neg=0, invalid=96777 setting smoothness coefficient to 1.000 blurring input image with Gaussian with sigma=2.000... 0000: dt=0.000, rms=0.426, neg=0, invalid=96777 0403: dt=0.000000, rms=0.426 (0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.426, neg=0, invalid=96777 0404: dt=0.000000, rms=0.426 (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=0.418, neg=0, invalid=96777 iter 0, gcam->neg = 406 after 8 iterations, nbhd size=1, neg = 0 0405: dt=0.715986, rms=0.406 (2.854%), neg=0, invalid=96777 0406: dt=0.000188, rms=0.406 (0.002%), neg=0, invalid=96777 0407: dt=0.000188, rms=0.406 (0.000%), neg=0, invalid=96777 0408: dt=0.000188, rms=0.406 (-0.000%), neg=0, invalid=96777 blurring input image with Gaussian with sigma=0.500... 0000: dt=0.000, rms=0.406, neg=0, invalid=96777 0409: dt=0.003000, rms=0.406 (0.003%), neg=0, invalid=96777 0410: dt=0.000109, rms=0.406 (0.000%), neg=0, invalid=96777 0411: dt=0.000109, rms=0.406 (0.000%), neg=0, invalid=96777 0412: dt=0.000109, rms=0.406 (0.000%), neg=0, invalid=96777 0413: dt=0.000109, rms=0.406 (0.001%), neg=0, invalid=96777 0414: dt=0.000109, rms=0.406 (0.001%), neg=0, invalid=96777 0415: dt=0.000109, rms=0.406 (0.001%), neg=0, invalid=96777 0416: dt=0.000109, rms=0.406 (0.001%), neg=0, invalid=96777 0417: dt=0.000109, rms=0.406 (0.001%), neg=0, invalid=96777 0418: dt=0.000109, rms=0.406 (0.001%), neg=0, invalid=96777 0419: dt=0.000109, rms=0.406 (0.001%), neg=0, invalid=96777 0420: dt=0.000109, rms=0.406 (0.001%), neg=0, invalid=96777 0421: dt=0.000109, rms=0.406 (0.001%), neg=0, invalid=96777 0422: dt=0.000109, rms=0.406 (0.001%), neg=0, invalid=96777 0423: dt=0.000109, rms=0.406 (0.001%), neg=0, invalid=96777 0424: dt=0.000109, rms=0.406 (0.001%), neg=0, invalid=96777 0425: dt=0.000109, rms=0.406 (0.001%), neg=0, invalid=96777 0426: dt=0.000109, rms=0.406 (0.002%), neg=0, invalid=96777 0427: dt=0.000109, rms=0.406 (0.002%), neg=0, invalid=96777 0428: dt=0.000109, rms=0.406 (0.002%), neg=0, invalid=96777 0429: dt=0.000109, rms=0.406 (0.002%), neg=0, invalid=96777 0430: dt=0.000109, rms=0.406 (0.002%), neg=0, invalid=96777 0431: dt=0.000109, rms=0.406 (0.002%), neg=0, invalid=96777 0432: dt=0.000109, rms=0.406 (0.002%), neg=0, invalid=96777 0433: dt=0.000109, rms=0.406 (0.002%), neg=0, invalid=96777 0434: dt=0.000109, rms=0.406 (0.002%), neg=0, invalid=96777 0435: dt=0.000109, rms=0.406 (0.002%), neg=0, invalid=96777 0436: dt=0.000109, rms=0.406 (0.002%), neg=0, invalid=96777 0437: dt=0.000109, rms=0.406 (0.002%), neg=0, invalid=96777 0438: dt=0.000109, rms=0.406 (0.002%), neg=0, invalid=96777 0439: dt=0.000109, rms=0.406 (0.002%), neg=0, invalid=96777 0440: dt=0.000109, rms=0.406 (0.002%), neg=0, invalid=96777 0441: dt=0.000109, rms=0.406 (0.002%), neg=0, invalid=96777 0442: dt=0.000109, rms=0.406 (0.002%), neg=0, invalid=96777 writing output transformation to transforms/talairach.m3z... GCAMwrite registration took 2 hours, 21 minutes and 32 seconds. #-------------------------------------- #@# CA Reg Inv Fri Mar 18 15:19:49 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/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 Mar 18 15:20:59 EDT 2016 mri_remove_neck -radius 25 nu.mgz transforms/talairach.m3z /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/RB_all_2008-03-26.gca nu_noneck.mgz erasing everything more than 25 mm from possible brain reading atlas '/neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/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... 12341890 nonbrain voxels erased writing output to nu_noneck.mgz... nonbrain removal took 1 minutes and 14 seconds. #-------------------------------------- #@# SkullLTA Fri Mar 18 15:22:13 EDT 2016 mri_em_register -skull -t transforms/talairach.lta nu_noneck.mgz /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/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 '/neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/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=15.0 skull bounding box = (60, 46, 44) --> (196, 190, 210) using (105, 94, 127) as brain centroid... mean wm in atlas = 126, using box (88,76,107) --> (121, 111,147) to find MRI wm before smoothing, mri peak at 110 after smoothing, mri peak at 109, scaling input intensities by 1.156 scaling channel 0 by 1.15596 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.167 0.044 0.003 -29.488; -0.041 1.367 -0.195 -0.759; -0.009 0.169 1.217 -59.769; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.167 0.044 0.003 -29.488; -0.041 1.367 -0.195 -0.759; -0.009 0.182 1.309 -72.204; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.0) 1.167 0.044 0.003 -29.488; -0.041 1.367 -0.195 -0.759; -0.009 0.182 1.309 -72.204; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.0) 1.210 0.002 0.050 -36.327; -0.002 1.379 -0.063 -23.355; -0.044 0.048 1.345 -60.961; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.210 0.002 0.050 -36.327; -0.002 1.379 -0.063 -23.355; -0.044 0.048 1.345 -60.961; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.206 0.024 0.037 -36.582; -0.021 1.373 -0.085 -18.008; -0.034 0.070 1.345 -64.840; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.206 0.024 0.037 -36.582; -0.021 1.373 -0.085 -18.008; -0.034 0.070 1.345 -64.840; 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 1.20630 0.02378 0.03735 -36.58156; -0.02096 1.37316 -0.08493 -18.00765; -0.03406 0.07039 1.34529 -64.83987; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.20630 0.02378 0.03735 -36.58156; -0.02096 1.37316 -0.08493 -18.00765; -0.03406 0.07039 1.34529 -64.83987; 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: 1.206 0.024 0.037 -36.582; -0.021 1.373 -0.085 -18.008; -0.034 0.070 1.345 -64.840; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.0 (old=-4.1) transform before final EM align: 1.206 0.024 0.037 -36.582; -0.021 1.373 -0.085 -18.008; -0.034 0.070 1.345 -64.840; 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 1.20630 0.02378 0.03735 -36.58156; -0.02096 1.37316 -0.08493 -18.00765; -0.03406 0.07039 1.34529 -64.83987; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.20630 0.02378 0.03735 -36.58156; -0.02096 1.37316 -0.08493 -18.00765; -0.03406 0.07039 1.34529 -64.83987; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 4.4 tol 0.000000 final transform: 1.206 0.024 0.037 -36.582; -0.021 1.373 -0.085 -18.008; -0.034 0.070 1.345 -64.840; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull_2.lta... registration took 32 minutes and 51 seconds. #-------------------------------------- #@# SubCort Seg Fri Mar 18 15:55:04 EDT 2016 mri_ca_label -align norm.mgz transforms/talairach.m3z /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz sysname Linux hostname rc-russia machine x86_64 setenv SUBJECTS_DIR /tmp/surfaKCaG0free/MRI cd /tmp/surfaKCaG0free/MRI/Freesurfer/mri mri_ca_label -align norm.mgz transforms/talairach.m3z /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/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 /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/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 /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/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 = 0.22932 ( 5) Left_Lateral_Ventricle (4): linear fit = 0.16 x + 0.0 (133 voxels, overlap=0.002) Left_Lateral_Ventricle (4): linear fit = 0.40 x + 0.0 (133 voxels, peak = 4), gca=10.8 gca peak = 0.14982 (20) mri peak = 0.16329 (13) Right_Lateral_Ventricle (43): linear fit = 0.54 x + 0.0 (100 voxels, overlap=0.772) Right_Lateral_Ventricle (43): linear fit = 0.54 x + 0.0 (100 voxels, peak = 11), gca=10.7 gca peak = 0.28003 (97) mri peak = 0.16063 (98) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (192 voxels, overlap=0.978) Right_Pallidum (52): linear fit = 0.98 x + 0.0 (192 voxels, peak = 95), gca=94.6 gca peak = 0.18160 (96) mri peak = 0.15146 (95) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (181 voxels, overlap=0.943) Left_Pallidum (13): linear fit = 0.94 x + 0.0 (181 voxels, peak = 90), gca=89.8 gca peak = 0.27536 (62) mri peak = 0.14391 (76) Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (603 voxels, overlap=0.018) Right_Hippocampus (53): linear fit = 1.21 x + 0.0 (603 voxels, peak = 75), gca=74.7 gca peak = 0.32745 (63) mri peak = 0.16517 (75) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (554 voxels, overlap=0.017) Left_Hippocampus (17): linear fit = 1.12 x + 0.0 (554 voxels, peak = 71), gca=70.9 gca peak = 0.08597 (105) mri peak = 0.11799 (109) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (13568 voxels, overlap=0.558) Right_Cerebral_White_Matter (41): linear fit = 1.03 x + 0.0 (13568 voxels, peak = 109), gca=108.7 gca peak = 0.09209 (106) mri peak = 0.10961 (110) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (14568 voxels, overlap=0.564) Left_Cerebral_White_Matter (2): linear fit = 1.03 x + 0.0 (14568 voxels, peak = 110), gca=109.7 gca peak = 0.07826 (63) mri peak = 0.05639 (71) Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (28293 voxels, overlap=0.693) Left_Cerebral_Cortex (3): linear fit = 1.10 x + 0.0 (28293 voxels, peak = 69), gca=69.0 gca peak = 0.08598 (64) mri peak = 0.06522 (70) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (29328 voxels, overlap=0.734) Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (29328 voxels, peak = 69), gca=68.8 gca peak = 0.24164 (71) mri peak = 0.16854 (82) Right_Caudate (50): linear fit = 1.11 x + 0.0 (356 voxels, overlap=0.013) Right_Caudate (50): linear fit = 1.11 x + 0.0 (356 voxels, peak = 78), gca=78.5 gca peak = 0.18227 (75) mri peak = 0.14985 (78) Left_Caudate (11): linear fit = 1.02 x + 0.0 (654 voxels, overlap=0.814) Left_Caudate (11): linear fit = 1.02 x + 0.0 (654 voxels, peak = 77), gca=76.9 gca peak = 0.10629 (62) mri peak = 0.05957 (72) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (21593 voxels, overlap=0.633) Left_Cerebellum_Cortex (8): linear fit = 1.12 x + 0.0 (21593 voxels, peak = 70), gca=69.8 gca peak = 0.11668 (59) mri peak = 0.06290 (69) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (21421 voxels, overlap=0.541) Right_Cerebellum_Cortex (47): linear fit = 1.15 x + 0.0 (21421 voxels, peak = 68), gca=68.1 gca peak = 0.17849 (88) mri peak = 0.08289 (98) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (2834 voxels, overlap=0.604) Left_Cerebellum_White_Matter (7): linear fit = 1.09 x + 0.0 (2834 voxels, peak = 95), gca=95.5 gca peak = 0.16819 (86) mri peak = 0.11462 (97) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (2808 voxels, overlap=0.486) Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (2808 voxels, peak = 92), gca=92.5 gca peak = 0.41688 (64) mri peak = 0.16418 (77) Left_Amygdala (18): linear fit = 1.20 x + 0.0 (198 voxels, overlap=0.041) Left_Amygdala (18): linear fit = 1.20 x + 0.0 (198 voxels, peak = 76), gca=76.5 gca peak = 0.42394 (62) mri peak = 0.17360 (78) Right_Amygdala (54): linear fit = 1.23 x + 0.0 (209 voxels, overlap=0.038) Right_Amygdala (54): linear fit = 1.23 x + 0.0 (209 voxels, peak = 76), gca=76.0 gca peak = 0.10041 (96) mri peak = 0.08176 (103) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (2642 voxels, overlap=0.564) Left_Thalamus_Proper (10): linear fit = 1.07 x + 0.0 (2642 voxels, peak = 102), gca=102.2 gca peak = 0.13978 (88) mri peak = 0.07518 (98) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (2381 voxels, overlap=0.586) Right_Thalamus_Proper (49): linear fit = 1.09 x + 0.0 (2381 voxels, peak = 95), gca=95.5 gca peak = 0.08514 (81) mri peak = 0.13127 (88) Left_Putamen (12): linear fit = 1.00 x + 0.0 (937 voxels, overlap=0.635) Left_Putamen (12): linear fit = 1.00 x + 0.0 (937 voxels, peak = 81), gca=81.0 gca peak = 0.09624 (82) mri peak = 0.12303 (85) Right_Putamen (51): linear fit = 1.02 x + 0.0 (1016 voxels, overlap=0.742) Right_Putamen (51): linear fit = 1.02 x + 0.0 (1016 voxels, peak = 84), gca=84.0 gca peak = 0.07543 (88) mri peak = 0.07872 (103) Brain_Stem (16): linear fit = 1.16 x + 0.0 (5658 voxels, overlap=0.312) Brain_Stem (16): linear fit = 1.16 x + 0.0 (5658 voxels, peak = 103), gca=102.5 gca peak = 0.12757 (95) mri peak = 0.12889 (106) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (555 voxels, overlap=0.406) Right_VentralDC (60): linear fit = 1.10 x + 0.0 (555 voxels, peak = 104), gca=104.0 gca peak = 0.17004 (92) mri peak = 0.10124 (102) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (588 voxels, overlap=0.581) Left_VentralDC (28): linear fit = 1.10 x + 0.0 (588 voxels, peak = 101), gca=100.7 gca peak = 0.21361 (36) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.26069 (23) mri peak = 0.23217 (14) Fourth_Ventricle (15): linear fit = 0.56 x + 0.0 (171 voxels, overlap=0.022) Fourth_Ventricle (15): linear fit = 0.56 x + 0.0 (171 voxels, peak = 13), gca=12.8 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 1.15 x + 0.0 estimating mean wm scale to be 1.03 x + 0.0 estimating mean csf scale to be 0.47 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt renormalizing by structure alignment.... renormalizing input #0 gca peak = 0.31597 (11) mri peak = 0.22932 ( 5) Left_Lateral_Ventricle (4): linear fit = 0.41 x + 0.0 (133 voxels, overlap=0.410) Left_Lateral_Ventricle (4): linear fit = 0.41 x + 0.0 (133 voxels, peak = 4), gca=4.5 gca peak = 0.27692 (11) mri peak = 0.16329 (13) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (100 voxels, overlap=1.001) Right_Lateral_Ventricle (43): linear fit = 1.03 x + 0.0 (100 voxels, peak = 11), gca=11.4 gca peak = 0.33219 (95) mri peak = 0.16063 (98) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (192 voxels, overlap=1.006) Right_Pallidum (52): linear fit = 1.00 x + 0.0 (192 voxels, peak = 95), gca=95.0 gca peak = 0.18623 (90) mri peak = 0.15146 (95) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (181 voxels, overlap=0.736) Left_Pallidum (13): linear fit = 1.04 x + 0.0 (181 voxels, peak = 94), gca=94.0 gca peak = 0.27152 (75) mri peak = 0.14391 (76) Right_Hippocampus (53): linear fit = 0.94 x + 0.0 (603 voxels, overlap=0.881) Right_Hippocampus (53): linear fit = 0.94 x + 0.0 (603 voxels, peak = 71), gca=70.9 gca peak = 0.29429 (71) mri peak = 0.16517 (75) Left_Hippocampus (17): linear fit = 1.03 x + 0.0 (554 voxels, overlap=1.003) Left_Hippocampus (17): linear fit = 1.03 x + 0.0 (554 voxels, peak = 73), gca=73.5 gca peak = 0.08273 (109) mri peak = 0.11799 (109) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (13568 voxels, overlap=0.693) Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (13568 voxels, peak = 109), gca=109.0 gca peak = 0.08544 (110) mri peak = 0.10961 (110) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (14568 voxels, overlap=0.685) Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (14568 voxels, peak = 110), gca=110.0 gca peak = 0.07182 (69) mri peak = 0.05639 (71) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (28293 voxels, overlap=0.874) Left_Cerebral_Cortex (3): linear fit = 1.00 x + 0.0 (28293 voxels, peak = 69), gca=69.0 gca peak = 0.08211 (69) mri peak = 0.06522 (70) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (29328 voxels, overlap=0.855) Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (29328 voxels, peak = 69), gca=69.0 gca peak = 0.21644 (81) mri peak = 0.16854 (82) Right_Caudate (50): linear fit = 1.01 x + 0.0 (356 voxels, overlap=1.002) Right_Caudate (50): linear fit = 1.01 x + 0.0 (356 voxels, peak = 82), gca=82.2 gca peak = 0.18185 (77) mri peak = 0.14985 (78) Left_Caudate (11): linear fit = 1.00 x + 0.0 (654 voxels, overlap=0.772) Left_Caudate (11): linear fit = 1.00 x + 0.0 (654 voxels, peak = 77), gca=77.0 gca peak = 0.09274 (69) mri peak = 0.05957 (72) Left_Cerebellum_Cortex (8): linear fit = 1.03 x + 0.0 (21593 voxels, overlap=0.983) Left_Cerebellum_Cortex (8): linear fit = 1.03 x + 0.0 (21593 voxels, peak = 71), gca=71.4 gca peak = 0.10875 (69) mri peak = 0.06290 (69) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (21421 voxels, overlap=0.995) Right_Cerebellum_Cortex (47): linear fit = 1.00 x + 0.0 (21421 voxels, peak = 69), gca=69.0 gca peak = 0.16774 (96) mri peak = 0.08289 (98) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (2834 voxels, overlap=0.989) Left_Cerebellum_White_Matter (7): linear fit = 1.02 x + 0.0 (2834 voxels, peak = 98), gca=98.4 gca peak = 0.16083 (93) mri peak = 0.11462 (97) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (2808 voxels, overlap=0.940) Right_Cerebellum_White_Matter (46): linear fit = 1.02 x + 0.0 (2808 voxels, peak = 95), gca=95.3 gca peak = 0.29993 (76) mri peak = 0.16418 (77) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (198 voxels, overlap=0.837) Left_Amygdala (18): linear fit = 0.99 x + 0.0 (198 voxels, peak = 75), gca=74.9 gca peak = 0.38365 (77) mri peak = 0.17360 (78) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (209 voxels, overlap=0.762) Right_Amygdala (54): linear fit = 1.00 x + 0.0 (209 voxels, peak = 77), gca=77.0 gca peak = 0.10757 (102) mri peak = 0.08176 (103) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2642 voxels, overlap=0.880) Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (2642 voxels, peak = 102), gca=102.0 gca peak = 0.11562 (95) mri peak = 0.07518 (98) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (2381 voxels, overlap=0.981) Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (2381 voxels, peak = 95), gca=95.5 gca peak = 0.08514 (81) mri peak = 0.13127 (88) Left_Putamen (12): linear fit = 1.00 x + 0.0 (937 voxels, overlap=0.635) Left_Putamen (12): linear fit = 1.00 x + 0.0 (937 voxels, peak = 81), gca=81.0 gca peak = 0.10117 (78) mri peak = 0.12303 (85) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1016 voxels, overlap=0.828) Right_Putamen (51): linear fit = 1.01 x + 0.0 (1016 voxels, peak = 79), gca=79.2 gca peak = 0.06370 (103) mri peak = 0.07872 (103) Brain_Stem (16): linear fit = 1.01 x + 0.0 (5658 voxels, overlap=0.798) Brain_Stem (16): linear fit = 1.01 x + 0.0 (5658 voxels, peak = 105), gca=104.5 gca peak = 0.11031 (100) mri peak = 0.12889 (106) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (555 voxels, overlap=0.678) Right_VentralDC (60): linear fit = 1.00 x + 0.0 (555 voxels, peak = 100), gca=100.0 gca peak = 0.15051 (101) mri peak = 0.10124 (102) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (588 voxels, overlap=0.867) Left_VentralDC (28): linear fit = 1.00 x + 0.0 (588 voxels, peak = 101), gca=101.0 gca peak = 0.30548 (17) uniform distribution in MR - rejecting arbitrary fit gca peak = 0.38725 (11) mri peak = 0.23217 (14) Fourth_Ventricle (15): linear fit = 1.23 x + 0.0 (171 voxels, overlap=0.958) Fourth_Ventricle (15): linear fit = 1.23 x + 0.0 (171 voxels, peak = 13), gca=13.5 gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.23325 (40) gca peak Third_Ventricle = 0.30548 (17) gca peak CSF = 0.27297 (19) gca peak Left_Accumbens_area = 0.36995 (71) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.63638 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.24517 (38) gca peak Right_Accumbens_area = 0.27366 (79) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.45329 (21) gca peak WM_hypointensities = 0.15026 (84) gca peak non_WM_hypointensities = 0.10275 (55) gca peak Optic_Chiasm = 0.34847 (76) not using caudate to estimate GM means estimating mean gm scale to be 0.99 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 0.89 x + 0.0 saving intensity scales to aseg.auto_noCCseg.label_intensities.txt saving sequentially combined intensity scales to aseg.auto_noCCseg.label_intensities.txt 13220 gm and wm labels changed (%34 to gray, %66 to white out of all changed labels) 177 hippocampal voxels changed. 0 amygdala voxels changed. pass 1: 52721 changed. image ll: -2.174, PF=1.000 pass 2: 9180 changed. pass 3: 3145 changed. writing labeled volume to aseg.auto_noCCseg.mgz... auto-labeling took 15 minutes and 39 seconds. mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /tmp/surfaKCaG0free/MRI/Freesurfer/mri/transforms/cc_up.lta Freesurfer will read input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will write lta as /tmp/surfaKCaG0free/MRI/Freesurfer/mri/transforms/cc_up.lta reading aseg from /tmp/surfaKCaG0free/MRI/Freesurfer/mri/aseg.auto_noCCseg.mgz reading norm from /tmp/surfaKCaG0free/MRI/Freesurfer/mri/norm.mgz 23259 voxels in left wm, 36651 in right wm, xrange [124, 132] searching rotation angles z=[-8 6], y=[-6 8] searching scale 1 Z rot -8.4 searching scale 1 Z rot -8.2 searching scale 1 Z rot -7.9 searching scale 1 Z rot -7.7 searching scale 1 Z rot -7.4 searching scale 1 Z rot -7.2 searching scale 1 Z rot -6.9 searching scale 1 Z rot -6.7 searching scale 1 Z rot -6.4 searching scale 1 Z rot -6.2 searching scale 1 Z rot -5.9 searching scale 1 Z rot -5.7 searching scale 1 Z rot -5.4 searching scale 1 Z rot -5.2 searching scale 1 Z rot -4.9 searching scale 1 Z rot -4.7 searching scale 1 Z rot -4.4 searching scale 1 Z rot -4.2 searching scale 1 Z rot -3.9 searching scale 1 Z rot -3.7 searching scale 1 Z rot -3.4 searching scale 1 Z rot -3.2 searching scale 1 Z rot -2.9 searching scale 1 Z rot -2.7 searching scale 1 Z rot -2.4 searching scale 1 Z rot -2.2 searching scale 1 Z rot -1.9 searching scale 1 Z rot -1.7 searching scale 1 Z rot -1.4 searching scale 1 Z rot -1.2 searching scale 1 Z rot -0.9 searching scale 1 Z rot -0.7 searching scale 1 Z rot -0.4 searching scale 1 Z rot -0.2 searching scale 1 Z rot 0.1 searching scale 1 Z rot 0.3 searching scale 1 Z rot 0.6 searching scale 1 Z rot 0.8 searching scale 1 Z rot 1.1 searching scale 1 Z rot 1.3 searching scale 1 Z rot 1.6 searching scale 1 Z rot 1.8 searching scale 1 Z rot 2.1 searching scale 1 Z rot 2.3 searching scale 1 Z rot 2.6 searching scale 1 Z rot 2.8 searching scale 1 Z rot 3.1 searching scale 1 Z rot 3.3 searching scale 1 Z rot 3.6 searching scale 1 Z rot 3.8 searching scale 1 Z rot 4.1 searching scale 1 Z rot 4.3 searching scale 1 Z rot 4.6 searching scale 1 Z rot 4.8 searching scale 1 Z rot 5.1 searching scale 1 Z rot 5.3 global minimum found at slice 128.3, rotations (1.45, -1.43) final transformation (x=128.3, yr=1.446, zr=-1.431): 0.999 0.025 0.025 -5.995; -0.025 1.000 -0.001 34.316; -0.025 -0.000 1.000 -1.721; 0.000 0.000 0.000 1.000; updating x range to be [127, 130] in xformed coordinates best xformed slice 128 cc center is found at 128 151 151 eigenvectors: -0.000 -0.004 1.000; 0.305 -0.952 -0.003; 0.952 0.305 0.001; error in mid anterior detected - correcting... writing aseg with callosum to /tmp/surfaKCaG0free/MRI/Freesurfer/mri/aseg.auto.mgz... corpus callosum matter segmentation took 0.6 minutes #-------------------------------------- #@# Merge ASeg Fri Mar 18 16:11:21 EDT 2016 cp aseg.auto.mgz aseg.mgz #-------------------------------------------- #@# Intensity Normalization2 Fri Mar 18 16:11:21 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/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... 1212 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 107 gm peak at 74 (74), valley at 34 (34) csf peak at 37, setting threshold to 61 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 74 (74), valley at 26 (26) csf peak at 37, setting threshold to 61 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to brain.mgz 3D bias adjustment took 3 minutes and 33 seconds. #-------------------------------------------- #@# Mask BFS Fri Mar 18 16:14:57 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 DoAbs = 0 Found 1149244 voxels in mask (pct= 6.85) Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Fri Mar 18 16:14:59 EDT 2016 mri_segment brain.mgz wm.seg.mgz doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (103.0): 101.9 +- 7.2 [80.0 --> 125.0] GM (75.0) : 73.7 +- 9.6 [30.0 --> 96.0] setting bottom of white matter range to 83.3 setting top of gray matter range to 92.9 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... 4406 sparsely connected voxels removed... thickening thin strands.... 20 segments, 4971 filled 6261 bright non-wm voxels segmented. 2382 diagonally connected voxels added... white matter segmentation took 1.6 minutes writing output to wm.seg.mgz... mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz wm.asegedit.mgz preserving editing changes in input volume... auto filling took 0.58 minutes reading wm segmentation from wm.seg.mgz... 34 voxels added to wm to prevent paths from MTL structures to cortex 4560 additional wm voxels added 0 additional wm voxels added SEG EDIT: 32739 voxels turned on, 32060 voxels turned off. propagating editing to output volume from wm.seg.mgz 115,126,128 old 0 new 0 115,126,128 old 0 new 0 writing edited volume to wm.asegedit.mgz.... mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz Iteration Number : 1 pass 1 (xy+): 17 found - 17 modified | TOTAL: 17 pass 2 (xy+): 0 found - 17 modified | TOTAL: 17 pass 1 (xy-): 18 found - 18 modified | TOTAL: 35 pass 2 (xy-): 0 found - 18 modified | TOTAL: 35 pass 1 (yz+): 36 found - 36 modified | TOTAL: 71 pass 2 (yz+): 0 found - 36 modified | TOTAL: 71 pass 1 (yz-): 30 found - 30 modified | TOTAL: 101 pass 2 (yz-): 0 found - 30 modified | TOTAL: 101 pass 1 (xz+): 24 found - 24 modified | TOTAL: 125 pass 2 (xz+): 0 found - 24 modified | TOTAL: 125 pass 1 (xz-): 18 found - 18 modified | TOTAL: 143 pass 2 (xz-): 0 found - 18 modified | TOTAL: 143 Iteration Number : 1 pass 1 (+++): 12 found - 12 modified | TOTAL: 12 pass 2 (+++): 0 found - 12 modified | TOTAL: 12 pass 1 (+++): 13 found - 13 modified | TOTAL: 25 pass 2 (+++): 0 found - 13 modified | TOTAL: 25 pass 1 (+++): 13 found - 13 modified | TOTAL: 38 pass 2 (+++): 0 found - 13 modified | TOTAL: 38 pass 1 (+++): 13 found - 13 modified | TOTAL: 51 pass 2 (+++): 0 found - 13 modified | TOTAL: 51 Iteration Number : 1 pass 1 (++): 104 found - 104 modified | TOTAL: 104 pass 2 (++): 0 found - 104 modified | TOTAL: 104 pass 1 (+-): 125 found - 125 modified | TOTAL: 229 pass 2 (+-): 0 found - 125 modified | TOTAL: 229 pass 1 (--): 99 found - 99 modified | TOTAL: 328 pass 2 (--): 1 found - 100 modified | TOTAL: 329 pass 3 (--): 0 found - 100 modified | TOTAL: 329 pass 1 (-+): 111 found - 111 modified | TOTAL: 440 pass 2 (-+): 0 found - 111 modified | TOTAL: 440 Iteration Number : 2 pass 1 (xy+): 3 found - 3 modified | TOTAL: 3 pass 2 (xy+): 0 found - 3 modified | TOTAL: 3 pass 1 (xy-): 2 found - 2 modified | TOTAL: 5 pass 2 (xy-): 0 found - 2 modified | TOTAL: 5 pass 1 (yz+): 0 found - 0 modified | TOTAL: 5 pass 1 (yz-): 1 found - 1 modified | TOTAL: 6 pass 2 (yz-): 0 found - 1 modified | TOTAL: 6 pass 1 (xz+): 4 found - 4 modified | TOTAL: 10 pass 2 (xz+): 0 found - 4 modified | TOTAL: 10 pass 1 (xz-): 7 found - 7 modified | TOTAL: 17 pass 2 (xz-): 0 found - 7 modified | TOTAL: 17 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 (+-): 1 found - 1 modified | TOTAL: 1 pass 2 (+-): 0 found - 1 modified | TOTAL: 1 pass 1 (--): 1 found - 1 modified | TOTAL: 2 pass 2 (--): 0 found - 1 modified | TOTAL: 2 pass 1 (-+): 0 found - 0 modified | TOTAL: 2 Iteration Number : 3 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 3 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 653 (out of 314467: 0.207653) binarizing input wm segmentation... Ambiguous edge configurations... mri_pretess done #-------------------------------------------- #@# Fill Fri Mar 18 16:17:13 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/mri mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz logging cutting plane coordinates to ../scripts/ponscc.cut.log... INFO: Using transforms/talairach.lta and its offset for Talairach volume ... using segmentation aseg.auto_noCCseg.mgz... reading input volume...done. searching for cutting planes...voxel to talairach voxel transform 1.167 0.044 0.003 -29.488; -0.039 1.285 -0.184 6.544; -0.008 0.157 1.133 -48.201; 0.000 0.000 0.000 1.000; voxel to talairach voxel transform 1.167 0.044 0.003 -29.488; -0.039 1.285 -0.184 6.544; -0.008 0.157 1.133 -48.201; 0.000 0.000 0.000 1.000; reading segmented volume aseg.auto_noCCseg.mgz... Looking for area (min, max) = (350, 1400) area[0] = 840 (min = 350, max = 1400), aspect = 0.38 (min = 0.10, max = 0.75) no need to search using seed (125, 119, 150), TAL = (3.0, 22.0, 9.0) talairach voxel to voxel transform 0.856 -0.029 -0.007 25.094; 0.026 0.762 0.123 1.735; 0.002 -0.106 0.866 42.497; 0.000 0.000 0.000 1.000; segmentation indicates cc at (125, 119, 150) --> (3.0, 22.0, 9.0) done. writing output to filled.mgz... filling took 0.8 minutes talairach cc position changed to (3.00, 22.00, 9.00) Erasing brainstem...done. seed_search_size = 9, min_neighbors = 5 search rh wm seed point around talairach space:(21.00, 22.00, 9.00) SRC: (112.25, 113.75, 160.01) search lh wm seed point around talairach space (-15.00, 22.00, 9.00), SRC: (143.07, 114.69, 160.10) 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 Mar 18 16:18:01 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz Iteration Number : 1 pass 1 (xy+): 1 found - 1 modified | TOTAL: 1 pass 2 (xy+): 0 found - 1 modified | TOTAL: 1 pass 1 (xy-): 2 found - 2 modified | TOTAL: 3 pass 2 (xy-): 0 found - 2 modified | TOTAL: 3 pass 1 (yz+): 2 found - 2 modified | TOTAL: 5 pass 2 (yz+): 0 found - 2 modified | TOTAL: 5 pass 1 (yz-): 2 found - 2 modified | TOTAL: 7 pass 2 (yz-): 0 found - 2 modified | TOTAL: 7 pass 1 (xz+): 0 found - 0 modified | TOTAL: 7 pass 1 (xz-): 3 found - 3 modified | TOTAL: 10 pass 2 (xz-): 0 found - 3 modified | TOTAL: 10 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 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 pass 1 (-+): 2 found - 2 modified | TOTAL: 3 pass 2 (-+): 0 found - 2 modified | TOTAL: 3 Iteration Number : 2 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 0 found - 0 modified | TOTAL: 0 pass 1 (yz-): 0 found - 0 modified | TOTAL: 0 pass 1 (xz+): 0 found - 0 modified | TOTAL: 0 pass 1 (xz-): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 2 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 Total Number of Modified Voxels = 13 (out of 148250: 0.008769) 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 60: 2518 vertices, 2663 faces slice 70: 7120 vertices, 7280 faces slice 80: 12162 vertices, 12388 faces slice 90: 18850 vertices, 19152 faces slice 100: 27066 vertices, 27394 faces slice 110: 36380 vertices, 36753 faces slice 120: 47213 vertices, 47659 faces slice 130: 57816 vertices, 58263 faces slice 140: 67932 vertices, 68340 faces slice 150: 76387 vertices, 76760 faces slice 160: 83250 vertices, 83590 faces slice 170: 89882 vertices, 90226 faces slice 180: 95530 vertices, 95816 faces slice 190: 100023 vertices, 100261 faces slice 200: 101180 vertices, 101296 faces slice 210: 101180 vertices, 101296 faces slice 220: 101180 vertices, 101296 faces slice 230: 101180 vertices, 101296 faces slice 240: 101180 vertices, 101296 faces slice 250: 101180 vertices, 101296 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... 101180 voxel in cpt #1: X=-116 [v=101180,e=303888,f=202592] located at (-24.857481, -5.329927, 25.245295) For the whole surface: X=-116 [v=101180,e=303888,f=202592] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 lh Fri Mar 18 16:18:07 EDT 2016 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix /tmp/surfaKCaG0free/MRI/Freesurfer/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 Mar 18 16:18:09 EDT 2016 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix /tmp/surfaKCaG0free/MRI/Freesurfer/scripts avg radius = 40.3 mm, total surface area = 52402 mm^2 writing inflated surface to ../surf/lh.inflated.nofix inflation took 0.3 minutes Not saving sulc step 000: RMS=0.115 (target=0.015) step 005: RMS=0.089 (target=0.015) step 010: RMS=0.072 (target=0.015) step 015: RMS=0.064 (target=0.015) step 020: RMS=0.060 (target=0.015) step 025: RMS=0.055 (target=0.015) step 030: RMS=0.053 (target=0.015) step 035: RMS=0.051 (target=0.015) step 040: RMS=0.050 (target=0.015) step 045: RMS=0.049 (target=0.015) step 050: RMS=0.049 (target=0.015) step 055: RMS=0.048 (target=0.015) step 060: RMS=0.048 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere lh Fri Mar 18 16:18:30 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.08 +- 0.80 (0.00-->10.88) (max @ vno 66345 --> 66346) face area 0.03 +- 0.05 (-0.31-->1.73) scaling brain by 0.354... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.454, avgs=0 005/300: dt: 0.9000, rms radial error=177.193, avgs=0 010/300: dt: 0.9000, rms radial error=176.634, avgs=0 015/300: dt: 0.9000, rms radial error=175.900, avgs=0 020/300: dt: 0.9000, rms radial error=175.064, avgs=0 025/300: dt: 0.9000, rms radial error=174.169, avgs=0 030/300: dt: 0.9000, rms radial error=173.240, avgs=0 035/300: dt: 0.9000, rms radial error=172.294, avgs=0 040/300: dt: 0.9000, rms radial error=171.340, avgs=0 045/300: dt: 0.9000, rms radial error=170.382, avgs=0 050/300: dt: 0.9000, rms radial error=169.425, avgs=0 055/300: dt: 0.9000, rms radial error=168.470, avgs=0 060/300: dt: 0.9000, rms radial error=167.519, avgs=0 065/300: dt: 0.9000, rms radial error=166.572, avgs=0 070/300: dt: 0.9000, rms radial error=165.629, avgs=0 075/300: dt: 0.9000, rms radial error=164.692, avgs=0 080/300: dt: 0.9000, rms radial error=163.759, avgs=0 085/300: dt: 0.9000, rms radial error=162.833, avgs=0 090/300: dt: 0.9000, rms radial error=161.912, avgs=0 095/300: dt: 0.9000, rms radial error=160.996, avgs=0 100/300: dt: 0.9000, rms radial error=160.085, avgs=0 105/300: dt: 0.9000, rms radial error=159.179, avgs=0 110/300: dt: 0.9000, rms radial error=158.277, avgs=0 115/300: dt: 0.9000, rms radial error=157.381, avgs=0 120/300: dt: 0.9000, rms radial error=156.490, avgs=0 125/300: dt: 0.9000, rms radial error=155.604, avgs=0 130/300: dt: 0.9000, rms radial error=154.722, avgs=0 135/300: dt: 0.9000, rms radial error=153.847, avgs=0 140/300: dt: 0.9000, rms radial error=152.976, avgs=0 145/300: dt: 0.9000, rms radial error=152.110, avgs=0 150/300: dt: 0.9000, rms radial error=151.248, avgs=0 155/300: dt: 0.9000, rms radial error=150.392, avgs=0 160/300: dt: 0.9000, rms radial error=149.540, avgs=0 165/300: dt: 0.9000, rms radial error=148.694, avgs=0 170/300: dt: 0.9000, rms radial error=147.851, avgs=0 175/300: dt: 0.9000, rms radial error=147.014, avgs=0 180/300: dt: 0.9000, rms radial error=146.181, avgs=0 185/300: dt: 0.9000, rms radial error=145.353, avgs=0 190/300: dt: 0.9000, rms radial error=144.530, avgs=0 195/300: dt: 0.9000, rms radial error=143.711, avgs=0 200/300: dt: 0.9000, rms radial error=142.897, avgs=0 205/300: dt: 0.9000, rms radial error=142.088, avgs=0 210/300: dt: 0.9000, rms radial error=141.283, avgs=0 215/300: dt: 0.9000, rms radial error=140.482, avgs=0 220/300: dt: 0.9000, rms radial error=139.687, avgs=0 225/300: dt: 0.9000, rms radial error=138.895, avgs=0 230/300: dt: 0.9000, rms radial error=138.108, avgs=0 235/300: dt: 0.9000, rms radial error=137.326, avgs=0 240/300: dt: 0.9000, rms radial error=136.548, avgs=0 245/300: dt: 0.9000, rms radial error=135.774, avgs=0 250/300: dt: 0.9000, rms radial error=135.005, avgs=0 255/300: dt: 0.9000, rms radial error=134.240, avgs=0 260/300: dt: 0.9000, rms radial error=133.480, avgs=0 265/300: dt: 0.9000, rms radial error=132.723, avgs=0 270/300: dt: 0.9000, rms radial error=131.971, avgs=0 275/300: dt: 0.9000, rms radial error=131.224, avgs=0 280/300: dt: 0.9000, rms radial error=130.480, avgs=0 285/300: dt: 0.9000, rms radial error=129.741, avgs=0 290/300: dt: 0.9000, rms radial error=129.006, avgs=0 295/300: dt: 0.9000, rms radial error=128.275, avgs=0 300/300: dt: 0.9000, rms radial error=127.549, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 11568.54 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00013 epoch 2 (K=40.0), pass 1, starting sse = 1998.84 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00019 epoch 3 (K=160.0), pass 1, starting sse = 253.50 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/10 = 0.00110 epoch 4 (K=640.0), pass 1, starting sse = 35.05 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.06/11 = 0.00531 final writing spherical brain to ../surf/lh.qsphere.nofix spherical transformation took 0.05 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology lh Fri Mar 18 16:21:13 EDT 2016 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 Freesurfer 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=-116 (nv=101180, nf=202592, ne=303888, g=59) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 15820 ambiguous faces found in tessellation segmenting defects... 65 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 60 into 58 64 defects to be corrected 0 vertices coincident reading input surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2599 (-4.6300) -vertex loglikelihood: -6.3445 (-3.1723) -normal dot loglikelihood: -3.5199 (-3.5199) -quad curv loglikelihood: -6.0865 (-3.0433) Total Loglikelihood : -25.2109 CORRECTING DEFECT 0 (vertices=137, convex hull=112) After retessellation of defect 0, euler #=-59 (92177,274154,181918) : difference with theory (-61) = -2 CORRECTING DEFECT 1 (vertices=214, convex hull=160) After retessellation of defect 1, euler #=-58 (92256,274463,182149) : difference with theory (-60) = -2 CORRECTING DEFECT 2 (vertices=44, convex hull=85) After retessellation of defect 2, euler #=-57 (92280,274569,182232) : difference with theory (-59) = -2 CORRECTING DEFECT 3 (vertices=77, convex hull=102) After retessellation of defect 3, euler #=-56 (92317,274728,182355) : difference with theory (-58) = -2 CORRECTING DEFECT 4 (vertices=37, convex hull=73) After retessellation of defect 4, euler #=-55 (92338,274822,182429) : difference with theory (-57) = -2 CORRECTING DEFECT 5 (vertices=6, convex hull=40) After retessellation of defect 5, euler #=-54 (92340,274839,182445) : difference with theory (-56) = -2 CORRECTING DEFECT 6 (vertices=60, convex hull=72) After retessellation of defect 6, euler #=-53 (92364,274944,182527) : difference with theory (-55) = -2 CORRECTING DEFECT 7 (vertices=11, convex hull=36) After retessellation of defect 7, euler #=-52 (92366,274957,182539) : difference with theory (-54) = -2 CORRECTING DEFECT 8 (vertices=37, convex hull=73) After retessellation of defect 8, euler #=-51 (92383,275039,182605) : difference with theory (-53) = -2 CORRECTING DEFECT 9 (vertices=1529, convex hull=295) After retessellation of defect 9, euler #=-50 (92996,277030,183984) : difference with theory (-52) = -2 CORRECTING DEFECT 10 (vertices=42, convex hull=80) After retessellation of defect 10, euler #=-49 (93024,277148,184075) : difference with theory (-51) = -2 CORRECTING DEFECT 11 (vertices=38, convex hull=76) After retessellation of defect 11, euler #=-48 (93040,277225,184137) : difference with theory (-50) = -2 CORRECTING DEFECT 12 (vertices=58, convex hull=86) After retessellation of defect 12, euler #=-47 (93073,277366,184246) : difference with theory (-49) = -2 CORRECTING DEFECT 13 (vertices=25, convex hull=24) Warning - incorrect dp selected!!!!(-92.235617 >= -92.235624 ) After retessellation of defect 13, euler #=-46 (93075,277380,184259) : difference with theory (-48) = -2 CORRECTING DEFECT 14 (vertices=70, convex hull=82) After retessellation of defect 14, euler #=-45 (93106,277505,184354) : difference with theory (-47) = -2 CORRECTING DEFECT 15 (vertices=1703, convex hull=105) After retessellation of defect 15, euler #=-44 (93336,278247,184867) : difference with theory (-46) = -2 CORRECTING DEFECT 16 (vertices=41, convex hull=80) After retessellation of defect 16, euler #=-43 (93354,278335,184938) : difference with theory (-45) = -2 CORRECTING DEFECT 17 (vertices=53, convex hull=87) After retessellation of defect 17, euler #=-42 (93367,278408,184999) : difference with theory (-44) = -2 CORRECTING DEFECT 18 (vertices=114, convex hull=101) After retessellation of defect 18, euler #=-41 (93424,278621,185156) : difference with theory (-43) = -2 CORRECTING DEFECT 19 (vertices=45, convex hull=58) After retessellation of defect 19, euler #=-40 (93443,278699,185216) : difference with theory (-42) = -2 CORRECTING DEFECT 20 (vertices=88, convex hull=120) After retessellation of defect 20, euler #=-39 (93502,278925,185384) : difference with theory (-41) = -2 CORRECTING DEFECT 21 (vertices=126, convex hull=76) After retessellation of defect 21, euler #=-38 (93546,279088,185504) : difference with theory (-40) = -2 CORRECTING DEFECT 22 (vertices=18, convex hull=31) Warning - incorrect dp selected!!!!(-99.333792 >= -99.333793 ) After retessellation of defect 22, euler #=-37 (93550,279109,185522) : difference with theory (-39) = -2 CORRECTING DEFECT 23 (vertices=22, convex hull=65) After retessellation of defect 23, euler #=-36 (93559,279160,185565) : difference with theory (-38) = -2 CORRECTING DEFECT 24 (vertices=13, convex hull=19) After retessellation of defect 24, euler #=-35 (93561,279172,185576) : difference with theory (-37) = -2 CORRECTING DEFECT 25 (vertices=57, convex hull=85) After retessellation of defect 25, euler #=-34 (93596,279307,185677) : difference with theory (-36) = -2 CORRECTING DEFECT 26 (vertices=6, convex hull=28) Warning - incorrect dp selected!!!!(-71.639638 >= -71.639639 ) After retessellation of defect 26, euler #=-33 (93597,279318,185688) : difference with theory (-35) = -2 CORRECTING DEFECT 27 (vertices=29, convex hull=46) After retessellation of defect 27, euler #=-32 (93605,279359,185722) : difference with theory (-34) = -2 CORRECTING DEFECT 28 (vertices=70, convex hull=108) After retessellation of defect 28, euler #=-31 (93617,279441,185793) : difference with theory (-33) = -2 CORRECTING DEFECT 29 (vertices=41, convex hull=74) After retessellation of defect 29, euler #=-30 (93642,279545,185873) : difference with theory (-32) = -2 CORRECTING DEFECT 30 (vertices=47, convex hull=80) After retessellation of defect 30, euler #=-29 (93678,279689,185982) : difference with theory (-31) = -2 CORRECTING DEFECT 31 (vertices=69, convex hull=81) After retessellation of defect 31, euler #=-28 (93721,279854,186105) : difference with theory (-30) = -2 CORRECTING DEFECT 32 (vertices=279, convex hull=93) After retessellation of defect 32, euler #=-27 (93738,279946,186181) : difference with theory (-29) = -2 CORRECTING DEFECT 33 (vertices=106, convex hull=69) After retessellation of defect 33, euler #=-26 (93747,280010,186237) : difference with theory (-28) = -2 CORRECTING DEFECT 34 (vertices=37, convex hull=47) After retessellation of defect 34, euler #=-25 (93768,280093,186300) : difference with theory (-27) = -2 CORRECTING DEFECT 35 (vertices=6, convex hull=27) After retessellation of defect 35, euler #=-24 (93769,280105,186312) : difference with theory (-26) = -2 CORRECTING DEFECT 36 (vertices=43, convex hull=93) After retessellation of defect 36, euler #=-23 (93801,280241,186417) : difference with theory (-25) = -2 CORRECTING DEFECT 37 (vertices=326, convex hull=102) After retessellation of defect 37, euler #=-22 (93846,280420,186552) : difference with theory (-24) = -2 CORRECTING DEFECT 38 (vertices=15, convex hull=17) After retessellation of defect 38, euler #=-21 (93847,280426,186558) : difference with theory (-23) = -2 CORRECTING DEFECT 39 (vertices=58, convex hull=40) After retessellation of defect 39, euler #=-20 (93855,280466,186591) : difference with theory (-22) = -2 CORRECTING DEFECT 40 (vertices=65, convex hull=84) After retessellation of defect 40, euler #=-19 (93869,280544,186656) : difference with theory (-21) = -2 CORRECTING DEFECT 41 (vertices=23, convex hull=55) After retessellation of defect 41, euler #=-18 (93885,280611,186708) : difference with theory (-20) = -2 CORRECTING DEFECT 42 (vertices=1161, convex hull=733) After retessellation of defect 42, euler #=-20 (94501,282854,188333) : difference with theory (-19) = 1 CORRECTING DEFECT 43 (vertices=308, convex hull=69) After retessellation of defect 43, euler #=-19 (94536,282991,188436) : difference with theory (-18) = 1 CORRECTING DEFECT 44 (vertices=102, convex hull=108) After retessellation of defect 44, euler #=-18 (94573,283148,188557) : difference with theory (-17) = 1 CORRECTING DEFECT 45 (vertices=38, convex hull=33) After retessellation of defect 45, euler #=-17 (94585,283197,188595) : difference with theory (-16) = 1 CORRECTING DEFECT 46 (vertices=29, convex hull=54) After retessellation of defect 46, euler #=-16 (94594,283246,188636) : difference with theory (-15) = 1 CORRECTING DEFECT 47 (vertices=209, convex hull=128) After retessellation of defect 47, euler #=-15 (94648,283471,188808) : difference with theory (-14) = 1 CORRECTING DEFECT 48 (vertices=37, convex hull=58) After retessellation of defect 48, euler #=-14 (94671,283565,188880) : difference with theory (-13) = 1 CORRECTING DEFECT 49 (vertices=73, convex hull=56) After retessellation of defect 49, euler #=-13 (94695,283660,188952) : difference with theory (-12) = 1 CORRECTING DEFECT 50 (vertices=115, convex hull=75) After retessellation of defect 50, euler #=-12 (94721,283773,189040) : difference with theory (-11) = 1 CORRECTING DEFECT 51 (vertices=6, convex hull=21) After retessellation of defect 51, euler #=-11 (94722,283783,189050) : difference with theory (-10) = 1 CORRECTING DEFECT 52 (vertices=55, convex hull=94) After retessellation of defect 52, euler #=-10 (94745,283893,189138) : difference with theory (-9) = 1 CORRECTING DEFECT 53 (vertices=68, convex hull=49) After retessellation of defect 53, euler #=-9 (94751,283935,189175) : difference with theory (-8) = 1 CORRECTING DEFECT 54 (vertices=24, convex hull=45) After retessellation of defect 54, euler #=-8 (94760,283977,189209) : difference with theory (-7) = 1 CORRECTING DEFECT 55 (vertices=35, convex hull=27) After retessellation of defect 55, euler #=-7 (94762,283994,189225) : difference with theory (-6) = 1 CORRECTING DEFECT 56 (vertices=212, convex hull=64) After retessellation of defect 56, euler #=-6 (94780,284076,189290) : difference with theory (-5) = 1 CORRECTING DEFECT 57 (vertices=41, convex hull=63) After retessellation of defect 57, euler #=-5 (94801,284161,189355) : difference with theory (-4) = 1 CORRECTING DEFECT 58 (vertices=454, convex hull=172) normal vector of length zero at vertex 100533 with 4 faces normal vector of length zero at vertex 100533 with 4 faces normal vector of length zero at vertex 100533 with 4 faces normal vector of length zero at vertex 100533 with 4 faces normal vector of length zero at vertex 100532 with 4 faces normal vector of length zero at vertex 100532 with 4 faces normal vector of length zero at vertex 100532 with 4 faces normal vector of length zero at vertex 100532 with 4 faces normal vector of length zero at vertex 100532 with 4 faces normal vector of length zero at vertex 100532 with 4 faces normal vector of length zero at vertex 100532 with 4 faces normal vector of length zero at vertex 100532 with 4 faces normal vector of length zero at vertex 100532 with 4 faces normal vector of length zero at vertex 100530 with 4 faces normal vector of length zero at vertex 100533 with 6 faces normal vector of length zero at vertex 100530 with 4 faces normal vector of length zero at vertex 100533 with 6 faces normal vector of length zero at vertex 100530 with 4 faces normal vector of length zero at vertex 100533 with 6 faces normal vector of length zero at vertex 100530 with 4 faces normal vector of length zero at vertex 100533 with 6 faces After retessellation of defect 58, euler #=-3 (94813,284283,189467) : difference with theory (-3) = 0 CORRECTING DEFECT 59 (vertices=50, convex hull=87) After retessellation of defect 59, euler #=-2 (94843,284410,189565) : difference with theory (-2) = 0 CORRECTING DEFECT 60 (vertices=42, convex hull=84) After retessellation of defect 60, euler #=-1 (94853,284474,189620) : difference with theory (-1) = 0 CORRECTING DEFECT 61 (vertices=30, convex hull=62) After retessellation of defect 61, euler #=0 (94867,284540,189673) : difference with theory (0) = 0 CORRECTING DEFECT 62 (vertices=32, convex hull=85) After retessellation of defect 62, euler #=1 (94884,284622,189739) : difference with theory (1) = 0 CORRECTING DEFECT 63 (vertices=42, convex hull=59) After retessellation of defect 63, euler #=2 (94903,284703,189802) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.90 +- 0.31 (0.03-->14.54) (max @ vno 86030 --> 88681) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.90 +- 0.31 (0.03-->14.54) (max @ vno 86030 --> 88681) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 206 mutations (33.8%), 403 crossovers (66.2%), 554 vertices were eliminated building final representation... 6277 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=94903, nf=189802, ne=284703, g=0) writing corrected surface to /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 44.6 minutes 0 defective edges removing intersecting faces 000: 1033 intersecting 001: 132 intersecting 002: 69 intersecting 003: 49 intersecting 004: 47 intersecting 005: 45 intersecting 006: 41 intersecting 007: 37 intersecting 008: 31 intersecting 009: 25 intersecting 010: 19 intersecting 011: 10 intersecting expanding nbhd size to 2 012: 10 intersecting expanding nbhd size to 3 013: 10 intersecting 014: 7 intersecting 015: 5 intersecting expanding nbhd size to 4 016: 12 intersecting 017: 3 intersecting 018: 2 intersecting mris_euler_number ../surf/lh.orig euler # = v-e+f = 2g-2: 94903 - 284703 + 189802 = 2 --> 0 holes F =2V-4: 189802 = 189806-4 (0) 2E=3F: 569406 = 569406 (0) total defect index = 0 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_remove_intersection ../surf/lh.orig ../surf/lh.orig intersection removal took 0.00 hours removing intersecting faces 000: 436 intersecting 001: 97 intersecting 002: 59 intersecting 003: 50 intersecting expanding nbhd size to 2 004: 50 intersecting 005: 47 intersecting 006: 36 intersecting 007: 32 intersecting expanding nbhd size to 3 008: 34 intersecting 009: 31 intersecting 010: 27 intersecting 011: 24 intersecting 012: 18 intersecting 013: 11 intersecting 014: 8 intersecting 015: 6 intersecting 016: 5 intersecting 017: 3 intersecting writing corrected surface to ../surf/lh.orig rm ../surf/lh.inflated #-------------------------------------------- #@# Make White Surf lh Fri Mar 18 17:06:03 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs Freesurfer 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 /tmp/surfaKCaG0free/MRI/Freesurfer/mri/filled.mgz... reading volume /tmp/surfaKCaG0free/MRI/Freesurfer/mri/brain.finalsurfs.mgz... reading volume /tmp/surfaKCaG0free/MRI/Freesurfer/mri/wm.mgz... 10279 bright wm thresholded. 4356 bright non-wm voxels segmented. reading original surface position from /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.orig... computing class statistics... border white: 173912 voxels (1.04%) border gray 218602 voxels (1.30%) WM (94.0): 95.6 +- 7.8 [70.0 --> 110.0] GM (84.0) : 82.9 +- 10.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 64.4 (was 70) setting MAX_BORDER_WHITE to 111.8 (was 105) setting MIN_BORDER_WHITE to 75.0 (was 85) setting MAX_CSF to 53.9 (was 40) setting MAX_GRAY to 96.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 69.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 43.3 (was 40) repositioning cortical surface to gray/white boundary reading volume /tmp/surfaKCaG0free/MRI/Freesurfer/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.26 (0.02-->8.68) (max @ vno 92871 --> 92935) face area 0.28 +- 0.15 (0.00-->8.43) mean absolute distance = 0.74 +- 0.96 2604 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=104, GM=75 mean inside = 95.0, mean outside = 80.4 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=84.3, 351 (349) missing vertices, mean dist 0.3 [0.7 (%34.8)->0.8 (%65.2))] %68 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=rc-ru, 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 +- 0.30 (0.09-->8.19) (max @ vno 92871 --> 92935) face area 0.28 +- 0.16 (0.00-->8.44) mean absolute distance = 0.38 +- 0.60 2223 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5044997.5, rms=13.20 001: dt: 0.5000, sse=5292084.0, rms=10.652 (0.000%) 002: dt: 0.5000, sse=5150735.5, rms=8.751 (0.000%) 003: dt: 0.5000, sse=5139274.5, rms=7.399 (0.000%) 004: dt: 0.5000, sse=5086356.0, rms=6.499 (0.000%) 005: dt: 0.5000, sse=5116545.5, rms=5.793 (0.000%) 006: dt: 0.5000, sse=5090968.5, rms=5.276 (0.000%) 007: dt: 0.5000, sse=5104022.0, rms=4.990 (0.000%) 008: dt: 0.5000, sse=5102904.5, rms=4.826 (0.000%) rms = 4.81, time step reduction 1 of 3 to 0.250... 009: dt: 0.5000, sse=5141540.5, rms=4.808 (0.000%) 010: dt: 0.2500, sse=3461779.8, rms=4.324 (0.000%) 011: dt: 0.2500, sse=3281644.5, rms=4.187 (0.000%) 012: dt: 0.2500, sse=3214670.8, rms=4.129 (0.000%) rms = 4.10, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3196461.5, rms=4.096 (0.000%) 014: dt: 0.1250, sse=3139261.8, rms=4.016 (0.000%) rms = 3.99, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=3118038.8, rms=3.994 (0.000%) positioning took 1.0 minutes inhibiting deformation at non-cortical midline structures... removing 4 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 4 vertex label from ripped group removing 2 vertex label from ripped group mean border=87.2, 349 (112) missing vertices, mean dist -0.2 [0.4 (%75.2)->0.3 (%24.8))] %79 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=rc-ru, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.29 (0.07-->8.05) (max @ vno 92871 --> 92935) face area 0.34 +- 0.20 (0.00-->10.09) mean absolute distance = 0.28 +- 0.43 2434 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3336744.0, rms=5.12 016: dt: 0.5000, sse=3717238.8, rms=4.035 (0.000%) 017: dt: 0.5000, sse=3875500.5, rms=3.871 (0.000%) 018: dt: 0.5000, sse=4123321.0, rms=3.813 (0.000%) rms = 3.88, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=3545673.0, rms=3.455 (0.000%) 020: dt: 0.2500, sse=3360975.0, rms=3.331 (0.000%) rms = 3.31, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=3304397.2, rms=3.313 (0.000%) 022: dt: 0.1250, sse=3248731.5, rms=3.254 (0.000%) rms = 3.24, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=3223829.0, rms=3.244 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 4 vertex label from ripped group removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group mean border=88.9, 353 (78) missing vertices, mean dist -0.1 [0.3 (%67.3)->0.3 (%32.7))] %84 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=rc-ru, 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 +- 0.29 (0.08-->7.89) (max @ vno 92871 --> 92935) face area 0.33 +- 0.19 (0.00-->9.61) mean absolute distance = 0.25 +- 0.37 2075 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3275445.2, rms=3.80 024: dt: 0.5000, sse=3713804.2, rms=3.663 (0.000%) 025: dt: 0.5000, sse=3737574.8, rms=3.564 (0.000%) rms = 3.67, time step reduction 1 of 3 to 0.250... 026: dt: 0.2500, sse=3449820.5, rms=3.211 (0.000%) 027: dt: 0.2500, sse=3385634.0, rms=3.113 (0.000%) rms = 3.08, time step reduction 2 of 3 to 0.125... 028: dt: 0.2500, sse=3360117.0, rms=3.081 (0.000%) 029: dt: 0.1250, sse=3297265.8, rms=2.999 (0.000%) rms = 2.97, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=3277792.8, rms=2.966 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group mean border=89.4, 346 (58) missing vertices, mean dist -0.0 [0.3 (%54.4)->0.2 (%45.6))] %86 local maxima, % 6 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=rc-ru, 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 /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white... writing smoothed curvature to lh.curv 000: dt: 0.0000, sse=3281874.8, rms=3.11 rms = 3.42, time step reduction 1 of 3 to 0.250... 031: dt: 0.2500, sse=3376089.5, rms=2.857 (0.000%) rms = 2.93, time step reduction 2 of 3 to 0.125... rms = 2.81, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=3389522.8, rms=2.812 (0.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... generating cortex label... 10 non-cortical segments detected only using segment with 1590 vertices erasing segment 1 (vno[0] = 39754) erasing segment 2 (vno[0] = 48879) erasing segment 3 (vno[0] = 50926) erasing segment 4 (vno[0] = 52900) erasing segment 5 (vno[0] = 57906) erasing segment 6 (vno[0] = 58744) erasing segment 7 (vno[0] = 63225) erasing segment 8 (vno[0] = 63953) erasing segment 9 (vno[0] = 63980) writing cortex label to /tmp/surfaKCaG0free/MRI/Freesurfer/label/lh.cortex.label... writing curvature file /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.curv writing smoothed area to lh.area writing curvature file /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.area vertex spacing 0.89 +- 0.30 (0.04-->7.88) (max @ vno 92871 --> 92935) face area 0.33 +- 0.19 (0.00-->9.56) refinement took 3.8 minutes #-------------------------------------------- #@# Smooth2 lh Fri Mar 18 17:09:48 EDT 2016 mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white ../surf/lh.smoothwm /tmp/surfaKCaG0free/MRI/Freesurfer/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 Mar 18 17:09:51 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 40.3 mm, total surface area = 57207 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 000: RMS=0.123 (target=0.015) step 005: RMS=0.090 (target=0.015) step 010: RMS=0.070 (target=0.015) step 015: RMS=0.060 (target=0.015) step 020: RMS=0.052 (target=0.015) step 025: RMS=0.044 (target=0.015) step 030: RMS=0.040 (target=0.015) step 035: RMS=0.035 (target=0.015) step 040: RMS=0.033 (target=0.015) step 045: RMS=0.030 (target=0.015) step 050: RMS=0.028 (target=0.015) step 055: RMS=0.026 (target=0.015) step 060: RMS=0.025 (target=0.015) inflation complete. inflation took 0.4 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 91 vertices thresholded to be in k1 ~ [-0.51 3.18], k2 ~ [-0.23 0.25] total integrated curvature = -0.137*4pi (-1.717) --> 1 handles ICI = 1.6, FI = 8.3, variation=165.920 87 vertices thresholded to be in [-0.30 0.05] writing Gaussian curvature to ../surf/lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.003 60 vertices thresholded to be in [-0.26 0.75] done. writing mean curvature to ../surf/lh.inflated.H...curvature mean = -0.024, std = 0.029 done. #----------------------------------------- #@# Curvature Stats lh Fri Mar 18 17:11:18 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm Freesurfer 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 [ Freesurfer/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 [ 192 ] Gb_filter = 0 WARN: S lookup min: -0.126981 WARN: S explicit min: 0.000000 vertex = 597 #-------------------------------------------- #@# Sphere lh Fri Mar 18 17:11:21 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/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 0.332... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=rc-ru, 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 %27.39 pass 1: epoch 2 of 3 starting distance error %27.18 unfolding complete - removing small folds... starting distance error %26.50 removing remaining folds... final distance error %26.55 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/lh.sphere spherical transformation took 0.68 hours #-------------------------------------------- #@# Surf Reg lh Fri Mar 18 17:52:27 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_register -curv ../surf/lh.sphere /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/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 /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/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=rc-ru, 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=rc-ru, 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 = 0.585 curvature mean = 0.024, std = 0.927 curvature mean = 0.024, std = 0.875 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (0.00, -16.00, 16.00) sse = 219953.0, tmin=0.6096 d=32.00 min @ (0.00, 0.00, 8.00) sse = 209192.6, tmin=1.2263 d=16.00 min @ (4.00, 4.00, 0.00) sse = 193991.5, tmin=1.8505 d=4.00 min @ (1.00, 0.00, 0.00) sse = 193895.8, tmin=3.2034 d=2.00 min @ (-0.50, 0.00, 0.50) sse = 193675.2, tmin=3.8408 d=0.50 min @ (0.00, -0.12, -0.12) sse = 193671.6, tmin=5.1150 tol=1.0e+00, sigma=0.5, host=rc-ru, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 5.12 min curvature mean = -0.027, std = 0.972 curvature mean = 0.010, std = 0.948 curvature mean = -0.034, std = 0.983 curvature mean = 0.004, std = 0.976 curvature mean = -0.035, std = 0.986 curvature mean = 0.001, std = 0.990 2 Reading smoothwm curvature mean = -0.053, std = 0.361 curvature mean = 0.002, std = 0.068 curvature mean = 0.075, std = 0.330 curvature mean = -0.000, std = 0.082 curvature mean = 0.050, std = 0.480 curvature mean = -0.001, std = 0.090 curvature mean = 0.029, std = 0.601 curvature mean = -0.001, std = 0.094 curvature mean = 0.009, std = 0.715 MRISregister() return, current seed 0 writing registered surface to ../surf/lh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white lh Fri Mar 18 18:07:57 EDT 2016 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 Mar 18 18:07:59 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mrisp_paint -a 5 /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/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 /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/lh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/lh.avg_curv... #----------------------------------------- #@# Cortical Parc lh Fri Mar 18 18:08:00 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 Freesurfer lh ../surf/lh.sphere.reg /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/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 /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/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... 792 labels changed using aseg relabeling using gibbs priors... 000: 2332 changed, 94903 examined... 001: 550 changed, 10019 examined... 002: 123 changed, 3018 examined... 003: 44 changed, 713 examined... 004: 15 changed, 263 examined... 005: 6 changed, 91 examined... 006: 3 changed, 43 examined... 007: 0 changed, 22 examined... 221 labels changed using aseg 000: 94 total segments, 52 labels (294 vertices) changed 001: 42 total segments, 4 labels (11 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 37 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 835 vertices marked for relabeling... 835 labels changed in reclassification. writing output to ../label/lh.aparc.annot... classification took 0 minutes and 36 seconds. #-------------------------------------------- #@# Make Pial Surf lh Fri Mar 18 18:08:36 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs Freesurfer 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 /tmp/surfaKCaG0free/MRI/Freesurfer/mri/filled.mgz... reading volume /tmp/surfaKCaG0free/MRI/Freesurfer/mri/brain.finalsurfs.mgz... reading volume /tmp/surfaKCaG0free/MRI/Freesurfer/mri/wm.mgz... 10279 bright wm thresholded. 4356 bright non-wm voxels segmented. reading original surface position from /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.orig... computing class statistics... border white: 173912 voxels (1.04%) border gray 218602 voxels (1.30%) WM (94.0): 95.6 +- 7.8 [70.0 --> 110.0] GM (84.0) : 82.9 +- 10.6 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 64.4 (was 70) setting MAX_BORDER_WHITE to 111.8 (was 105) setting MIN_BORDER_WHITE to 75.0 (was 85) setting MAX_CSF to 53.9 (was 40) setting MAX_GRAY to 96.2 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 69.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 43.3 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=75 mean inside = 95.0, mean outside = 80.4 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 /tmp/surfaKCaG0free/MRI/Freesurfer/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.82 +- 0.26 (0.02-->8.68) (max @ vno 92871 --> 92935) face area 0.28 +- 0.15 (0.00-->8.43) mean absolute distance = 0.75 +- 1.00 2523 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 197 points - only 39.09% unknown deleting segment 2 with 14 points - only 0.00% unknown deleting segment 3 with 12 points - only 0.00% unknown deleting segment 4 with 21 points - only 0.00% unknown deleting segment 6 with 36 points - only 0.00% unknown deleting segment 7 with 83 points - only 0.00% unknown deleting segment 8 with 13 points - only 0.00% unknown deleting segment 9 with 592 points - only 0.00% unknown deleting segment 10 with 22 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 12 with 4 points - only 0.00% unknown deleting segment 13 with 12 points - only 0.00% unknown deleting segment 14 with 8 points - only 0.00% unknown deleting segment 15 with 7 points - only 0.00% unknown deleting segment 16 with 15 points - only 0.00% unknown deleting segment 17 with 6 points - only 0.00% unknown deleting segment 18 with 6 points - only 0.00% unknown deleting segment 19 with 63 points - only 0.00% unknown deleting segment 20 with 60 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 21 with 4 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 22 with 2 points - only 0.00% unknown mean border=84.4, 407 (365) missing vertices, mean dist 0.2 [0.7 (%35.1)->0.8 (%64.9))] %69 local maxima, %25 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=rc-ru, 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 +- 0.30 (0.08-->8.18) (max @ vno 92871 --> 92935) face area 0.28 +- 0.16 (0.00-->8.46) mean absolute distance = 0.39 +- 0.63 2237 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5254290.5, rms=13.51 001: dt: 0.5000, sse=5479032.0, rms=10.976 (0.000%) 002: dt: 0.5000, sse=5309679.0, rms=9.060 (0.000%) 003: dt: 0.5000, sse=5279323.0, rms=7.677 (0.000%) 004: dt: 0.5000, sse=5200023.0, rms=6.751 (0.000%) 005: dt: 0.5000, sse=5229697.5, rms=6.026 (0.000%) 006: dt: 0.5000, sse=5196602.5, rms=5.532 (0.000%) 007: dt: 0.5000, sse=5221750.0, rms=5.242 (0.000%) 008: dt: 0.5000, sse=5208368.0, rms=5.089 (0.000%) 009: dt: 0.5000, sse=5256280.5, rms=5.024 (0.000%) rms = 4.98, time step reduction 1 of 3 to 0.250... 010: dt: 0.5000, sse=5231013.5, rms=4.985 (0.000%) 011: dt: 0.2500, sse=3544770.8, rms=4.492 (0.000%) 012: dt: 0.2500, sse=3377942.2, rms=4.389 (0.000%) rms = 4.37, time step reduction 2 of 3 to 0.125... 013: dt: 0.2500, sse=3297056.8, rms=4.368 (0.000%) 014: dt: 0.1250, sse=3226427.0, rms=4.262 (0.000%) rms = 4.23, time step reduction 3 of 3 to 0.062... 015: dt: 0.1250, sse=3206355.2, rms=4.228 (0.000%) positioning took 1.1 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 214 points - only 35.98% unknown deleting segment 1 with 104 points - only 0.00% unknown deleting segment 2 with 26 points - only 0.00% unknown deleting segment 3 with 52 points - only 0.00% unknown deleting segment 7 with 111 points - only 0.00% unknown deleting segment 10 with 7 points - only 0.00% unknown deleting segment 11 with 108 points - only 0.00% unknown deleting segment 12 with 449 points - only 0.00% unknown deleting segment 13 with 14 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 15 with 13 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 17 with 36 points - only 0.00% unknown deleting segment 19 with 10 points - only 0.00% unknown deleting segment 20 with 46 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 22 with 4 points - only 0.00% unknown deleting segment 23 with 44 points - only 0.00% unknown deleting segment 24 with 56 points - only 0.00% unknown deleting segment 25 with 82 points - only 0.00% unknown deleting segment 26 with 5 points - only 0.00% unknown deleting segment 27 with 71 points - only 0.00% unknown mean border=87.3, 443 (119) missing vertices, mean dist -0.2 [0.4 (%75.2)->0.3 (%24.8))] %80 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=rc-ru, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.29 (0.06-->8.07) (max @ vno 92871 --> 92935) face area 0.35 +- 0.19 (0.00-->10.14) mean absolute distance = 0.29 +- 0.45 2362 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3529776.5, rms=5.61 016: dt: 0.5000, sse=3934557.2, rms=4.728 (0.000%) 017: dt: 0.5000, sse=4081859.8, rms=4.533 (0.000%) rms = 4.55, time step reduction 1 of 3 to 0.250... 018: dt: 0.2500, sse=3696329.2, rms=4.247 (0.000%) 019: dt: 0.2500, sse=3569471.8, rms=4.141 (0.000%) rms = 4.12, time step reduction 2 of 3 to 0.125... 020: dt: 0.2500, sse=3506907.0, rms=4.120 (0.000%) 021: dt: 0.1250, sse=3440926.8, rms=4.002 (0.000%) rms = 3.99, time step reduction 3 of 3 to 0.062... 022: dt: 0.1250, sse=3422771.8, rms=3.989 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 219 points - only 35.16% unknown deleting segment 1 with 125 points - only 0.00% unknown deleting segment 2 with 29 points - only 0.00% unknown deleting segment 3 with 12 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 109 points - only 0.00% unknown deleting segment 6 with 109 points - only 0.00% unknown deleting segment 7 with 537 points - only 0.00% unknown deleting segment 8 with 14 points - only 0.00% unknown deleting segment 9 with 14 points - only 0.00% unknown deleting segment 10 with 34 points - only 0.00% unknown deleting segment 11 with 10 points - only 0.00% unknown deleting segment 12 with 42 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 13 with 3 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 14 with 3 points - only 0.00% unknown deleting segment 15 with 44 points - only 0.00% unknown deleting segment 16 with 58 points - only 0.00% unknown deleting segment 17 with 19 points - only 0.00% unknown deleting segment 18 with 7 points - only 0.00% unknown deleting segment 19 with 92 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 20 with 3 points - only 0.00% unknown deleting segment 21 with 74 points - only 0.00% unknown deleting segment 22 with 26 points - only 0.00% unknown removing 4 vertex label from ripped group deleting segment 23 with 4 points - only 0.00% unknown mean border=88.9, 459 (81) missing vertices, mean dist -0.1 [0.3 (%67.6)->0.3 (%32.4))] %85 local maxima, % 9 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=rc-ru, nav=1, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.250 vertex spacing 0.90 +- 0.29 (0.07-->7.91) (max @ vno 92871 --> 92935) face area 0.34 +- 0.19 (0.00-->9.60) mean absolute distance = 0.25 +- 0.38 2274 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3487973.8, rms=4.50 023: dt: 0.5000, sse=3909308.5, rms=4.360 (0.000%) 024: dt: 0.5000, sse=3993786.0, rms=4.255 (0.000%) rms = 4.41, time step reduction 1 of 3 to 0.250... 025: dt: 0.2500, sse=3676035.2, rms=3.949 (0.000%) rms = 3.90, time step reduction 2 of 3 to 0.125... 026: dt: 0.2500, sse=3626758.2, rms=3.901 (0.000%) 027: dt: 0.1250, sse=3542292.8, rms=3.765 (0.000%) rms = 3.74, time step reduction 3 of 3 to 0.062... 028: dt: 0.1250, sse=3518262.2, rms=3.742 (0.000%) positioning took 0.5 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 199 points - only 35.18% unknown removing 1 vertex label from ripped group deleting segment 1 with 1 points - only 0.00% unknown deleting segment 2 with 50 points - only 0.00% unknown deleting segment 3 with 26 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 42 points - only 0.00% unknown deleting segment 6 with 61 points - only 0.00% unknown deleting segment 7 with 109 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 10 with 108 points - only 0.00% unknown deleting segment 11 with 558 points - only 0.00% unknown deleting segment 12 with 14 points - only 0.00% unknown deleting segment 13 with 14 points - only 0.00% unknown deleting segment 14 with 37 points - only 0.00% unknown deleting segment 15 with 10 points - only 0.00% unknown deleting segment 16 with 40 points - only 0.00% unknown deleting segment 17 with 8 points - only 0.00% unknown deleting segment 18 with 67 points - only 0.00% unknown deleting segment 19 with 38 points - only 0.00% unknown deleting segment 20 with 19 points - only 0.00% unknown deleting segment 21 with 7 points - only 0.00% unknown deleting segment 22 with 92 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 23 with 3 points - only 0.00% unknown deleting segment 24 with 78 points - only 0.00% unknown mean border=89.4, 512 (68) missing vertices, mean dist -0.0 [0.3 (%54.6)->0.2 (%45.4))] %87 local maxima, % 7 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=rc-ru, 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=3521885.2, rms=3.81 rms = 4.15, time step reduction 1 of 3 to 0.250... 029: dt: 0.2500, sse=3615808.5, rms=3.599 (0.000%) rms = 3.65, time step reduction 2 of 3 to 0.125... rms = 3.56, time step reduction 3 of 3 to 0.062... 030: dt: 0.1250, sse=3625210.8, rms=3.560 (0.000%) positioning took 0.2 minutes inhibiting deformation at non-cortical midline structures... smoothing surface for 5 iterations... mean border=65.2, 523 (523) missing vertices, mean dist 1.8 [1.2 (%0.4)->3.1 (%99.6))] %17 local maxima, %40 large gradients and %37 min vals, 2266 gradients ignored tol=1.0e-04, sigma=2.0, host=rc-ru, 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=12937295.0, rms=24.64 001: dt: 0.5000, sse=10287784.0, rms=21.353 (0.000%) 002: dt: 0.5000, sse=8340696.5, rms=18.586 (0.000%) 003: dt: 0.5000, sse=7043812.0, rms=16.398 (0.000%) 004: dt: 0.5000, sse=6264500.0, rms=14.694 (0.000%) 005: dt: 0.5000, sse=5793527.5, rms=13.393 (0.000%) 006: dt: 0.5000, sse=5466025.5, rms=12.390 (0.000%) 007: dt: 0.5000, sse=5270642.5, rms=11.613 (0.000%) 008: dt: 0.5000, sse=5165567.0, rms=10.932 (0.000%) 009: dt: 0.5000, sse=5116724.5, rms=10.383 (0.000%) 010: dt: 0.5000, sse=5057758.0, rms=9.839 (0.000%) 011: dt: 0.5000, sse=5061640.0, rms=9.361 (0.000%) 012: dt: 0.5000, sse=5069969.5, rms=8.911 (0.000%) 013: dt: 0.5000, sse=5129683.5, rms=8.515 (0.000%) 014: dt: 0.5000, sse=5099293.0, rms=8.100 (0.000%) 015: dt: 0.5000, sse=5213373.5, rms=7.720 (0.000%) 016: dt: 0.5000, sse=5178945.0, rms=7.289 (0.000%) 017: dt: 0.5000, sse=5246875.0, rms=6.918 (0.000%) 018: dt: 0.5000, sse=5270339.5, rms=6.555 (0.000%) 019: dt: 0.5000, sse=5316620.0, rms=6.312 (0.000%) 020: dt: 0.5000, sse=5333959.0, rms=6.083 (0.000%) 021: dt: 0.5000, sse=5413116.0, rms=5.932 (0.000%) 022: dt: 0.5000, sse=5395486.0, rms=5.798 (0.000%) 023: dt: 0.5000, sse=5416973.0, rms=5.692 (0.000%) 024: dt: 0.5000, sse=5421688.0, rms=5.629 (0.000%) 025: dt: 0.5000, sse=5480855.0, rms=5.577 (0.000%) 026: dt: 0.5000, sse=5446925.5, rms=5.492 (0.000%) rms = 5.49, time step reduction 1 of 3 to 0.250... 027: dt: 0.5000, sse=5464007.5, rms=5.490 (0.000%) 028: dt: 0.2500, sse=4420332.0, rms=4.979 (0.000%) 029: dt: 0.2500, sse=4318776.5, rms=4.818 (0.000%) rms = 4.84, time step reduction 2 of 3 to 0.125... 030: dt: 0.1250, sse=4228223.0, rms=4.709 (0.000%) positioning took 2.2 minutes mean border=63.3, 3151 (283) missing vertices, mean dist 0.2 [0.3 (%39.6)->0.8 (%60.4))] %35 local maxima, %28 large gradients and %29 min vals, 1243 gradients ignored tol=1.0e-04, sigma=1.0, host=rc-ru, 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=4791998.0, rms=6.16 031: dt: 0.5000, sse=5190862.0, rms=6.029 (0.000%) 032: dt: 0.5000, sse=5774039.0, rms=5.478 (0.000%) rms = 5.79, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=5114263.0, rms=4.970 (0.000%) rms = 4.95, time step reduction 2 of 3 to 0.125... 034: dt: 0.2500, sse=4893593.0, rms=4.947 (0.000%) 035: dt: 0.1250, sse=4673594.5, rms=4.710 (0.000%) 036: dt: 0.1250, sse=4637262.5, rms=4.615 (0.000%) rms = 4.60, time step reduction 3 of 3 to 0.062... 037: dt: 0.1250, sse=4649231.5, rms=4.602 (0.000%) positioning took 0.6 minutes mean border=62.3, 3399 (255) missing vertices, mean dist 0.2 [0.2 (%36.8)->0.5 (%63.2))] %45 local maxima, %17 large gradients and %30 min vals, 1354 gradients ignored tol=1.0e-04, sigma=0.5, host=rc-ru, 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=4708665.0, rms=4.83 rms = 5.52, time step reduction 1 of 3 to 0.250... 038: dt: 0.2500, sse=4614146.5, rms=4.619 (0.000%) rms = 4.63, time step reduction 2 of 3 to 0.125... rms = 4.57, time step reduction 3 of 3 to 0.062... 039: dt: 0.1250, sse=4589517.5, rms=4.573 (0.000%) positioning took 0.3 minutes mean border=61.9, 4726 (248) missing vertices, mean dist 0.1 [0.2 (%35.8)->0.4 (%64.2))] %47 local maxima, %14 large gradients and %29 min vals, 1373 gradients ignored tol=1.0e-04, sigma=0.2, host=rc-ru, 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 /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.pial... writing smoothed curvature to lh.curv.pial 000: dt: 0.0000, sse=4604071.0, rms=4.67 rms = 5.06, time step reduction 1 of 3 to 0.250... 040: dt: 0.2500, sse=4597088.0, rms=4.476 (0.000%) 041: dt: 0.2500, sse=4858698.0, rms=4.410 (0.000%) rms = 4.61, time step reduction 2 of 3 to 0.125... 042: dt: 0.1250, sse=4810522.5, rms=4.314 (0.000%) 043: dt: 0.1250, sse=4812097.0, rms=4.227 (0.000%) 044: dt: 0.1250, sse=4856736.5, rms=4.138 (0.000%) rms = 4.10, time step reduction 3 of 3 to 0.062... 045: dt: 0.1250, sse=4927201.0, rms=4.096 (0.000%) positioning took 0.6 minutes writing curvature file /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.curv.pial writing smoothed area to lh.area.pial writing curvature file /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.area.pial vertex spacing 1.10 +- 0.52 (0.08-->7.80) (max @ vno 66013 --> 65296) face area 0.47 +- 0.41 (0.00-->9.60) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 94903 vertices processed 25000 of 94903 vertices processed 50000 of 94903 vertices processed 75000 of 94903 vertices processed 0 of 94903 vertices processed 25000 of 94903 vertices processed 50000 of 94903 vertices processed 75000 of 94903 vertices processed thickness calculation complete, 1970:6805 truncations. 16334 vertices at 0 distance 46817 vertices at 1 distance 52812 vertices at 2 distance 35519 vertices at 3 distance 17363 vertices at 4 distance 6644 vertices at 5 distance 2377 vertices at 6 distance 972 vertices at 7 distance 465 vertices at 8 distance 280 vertices at 9 distance 200 vertices at 10 distance 168 vertices at 11 distance 121 vertices at 12 distance 90 vertices at 13 distance 94 vertices at 14 distance 90 vertices at 15 distance 75 vertices at 16 distance 66 vertices at 17 distance 41 vertices at 18 distance 48 vertices at 19 distance 70 vertices at 20 distance writing curvature file /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.thickness positioning took 8.1 minutes #-------------------------------------------- #@# Surf Volume lh Fri Mar 18 18:16:41 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/surf mris_calc -o lh.area.mid lh.area add lh.area.pial Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.area.mid lh.area.mid div 2 Saving result to 'lh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o lh.volume lh.area.mid mul lh.thickness Saving result to 'lh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast lh Fri Mar 18 18:16:42 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts pctsurfcon --s Freesurfer --lh-only Log file is /tmp/surfaKCaG0free/MRI/Freesurfer/scripts/pctsurfcon.log Fri Mar 18 18:16:42 EDT 2016 setenv SUBJECTS_DIR /tmp/surfaKCaG0free/MRI cd /tmp/surfaKCaG0free/MRI/Freesurfer/scripts /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux rc-russia 3.14.8-mosix #1 SMP Thu Jun 19 12:56:58 EDT 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 mri_vol2surf --mov /tmp/surfaKCaG0free/MRI/Freesurfer/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --projdist -1 --o /tmp/surfaKCaG0free/MRI/Freesurfer/surf/tmp.pctsurfcon.16391/lh.wm.mgh --regheader Freesurfer --cortex srcvol = /tmp/surfaKCaG0free/MRI/Freesurfer/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /tmp/surfaKCaG0free/MRI/Freesurfer/mri/orig.mgz as target reference. Loading label /tmp/surfaKCaG0free/MRI/Freesurfer/label/lh.cortex.label Reading surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 48642 Masking with /tmp/surfaKCaG0free/MRI/Freesurfer/label/lh.cortex.label Writing to /tmp/surfaKCaG0free/MRI/Freesurfer/surf/tmp.pctsurfcon.16391/lh.wm.mgh Dim: 94903 1 1 mri_vol2surf --mov /tmp/surfaKCaG0free/MRI/Freesurfer/mri/rawavg.mgz --hemi lh --noreshape --interp trilinear --o /tmp/surfaKCaG0free/MRI/Freesurfer/surf/tmp.pctsurfcon.16391/lh.gm.mgh --projfrac 0.3 --regheader Freesurfer --cortex srcvol = /tmp/surfaKCaG0free/MRI/Freesurfer/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /tmp/surfaKCaG0free/MRI/Freesurfer/mri/orig.mgz as target reference. Loading label /tmp/surfaKCaG0free/MRI/Freesurfer/label/lh.cortex.label Reading surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Done reading source surface Reading thickness /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 61789 Masking with /tmp/surfaKCaG0free/MRI/Freesurfer/label/lh.cortex.label Writing to /tmp/surfaKCaG0free/MRI/Freesurfer/surf/tmp.pctsurfcon.16391/lh.gm.mgh Dim: 94903 1 1 mri_concat /tmp/surfaKCaG0free/MRI/Freesurfer/surf/tmp.pctsurfcon.16391/lh.wm.mgh /tmp/surfaKCaG0free/MRI/Freesurfer/surf/tmp.pctsurfcon.16391/lh.gm.mgh --paired-diff-norm --mul 100 --o /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.w-g.pct.mgh mri_segstats --in /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.w-g.pct.mgh --annot Freesurfer lh aparc --sum /tmp/surfaKCaG0free/MRI/Freesurfer/stats/lh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --in /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.w-g.pct.mgh --annot Freesurfer lh aparc --sum /tmp/surfaKCaG0free/MRI/Freesurfer/stats/lh.w-g.pct.stats --snr sysname Linux hostname rc-russia machine x86_64 user rudolphpienaar UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 1000 Loading /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.w-g.pct.mgh Vertex Area is 0.662504 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 1000 unknown 0 0.000 1 1001 bankssts 1012 665.237 2 1002 caudalanteriorcingulate 503 317.796 3 1003 caudalmiddlefrontal 2970 1964.172 4 1004 corpuscallosum 0 0.000 5 1005 cuneus 1390 928.328 6 1006 entorhinal 341 221.111 7 1007 fusiform 2621 1718.420 8 1008 inferiorparietal 3832 2489.798 9 1009 inferiortemporal 3203 2202.714 10 1010 isthmuscingulate 681 433.073 11 1011 lateraloccipital 5953 3798.338 12 1012 lateralorbitofrontal 2844 1902.319 13 1013 lingual 3271 2189.725 14 1014 medialorbitofrontal 1892 1280.500 15 1015 middletemporal 3406 2290.284 16 1016 parahippocampal 770 490.682 17 1017 paracentral 2009 1261.919 18 1018 parsopercularis 1498 986.473 19 1019 parsorbitalis 843 532.385 20 1020 parstriangularis 1331 858.387 21 1021 pericalcarine 1454 974.632 22 1022 postcentral 5129 3366.922 23 1023 posteriorcingulate 963 641.891 24 1024 precentral 5556 3752.854 25 1025 precuneus 4264 2876.411 26 1026 rostralanteriorcingulate 927 625.612 27 1027 rostralmiddlefrontal 5983 3863.622 28 1028 superiorfrontal 7401 4966.189 29 1029 superiorparietal 6828 4801.575 30 1030 superiortemporal 3394 2190.341 31 1031 supramarginal 2817 1900.802 32 1032 frontalpole 224 157.234 33 1033 temporalpole 493 386.911 34 1034 transversetemporal 454 279.066 35 1035 insula 2163 1452.460 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats lh Fri Mar 18 18:16:46 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab Freesurfer lh white computing statistics for each annotation in ../label/lh.aparc.annot. reading volume /tmp/surfaKCaG0free/MRI/Freesurfer/mri/wm.mgz... reading input surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white... reading input pial surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.pial... reading input white surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1012 665 1766 2.858 0.501 0.107 0.027 7 1.1 bankssts 503 318 1540 3.986 1.157 0.136 0.046 10 1.0 caudalanteriorcingulate 2970 1964 7540 2.787 1.144 0.174 0.164 111 13.9 caudalmiddlefrontal 1390 928 2731 2.450 0.627 0.191 0.111 38 5.8 cuneus 341 221 1096 3.429 0.718 0.140 0.058 5 0.7 entorhinal 2621 1718 6879 3.293 0.777 0.146 0.068 69 7.5 fusiform 3832 2490 8289 2.532 0.967 0.166 0.204 218 22.1 inferiorparietal 3203 2203 9822 3.329 0.841 0.163 0.097 133 9.6 inferiortemporal 681 433 1396 3.208 1.158 0.167 0.071 15 1.9 isthmuscingulate 5953 3798 8933 2.094 0.724 0.155 0.076 118 18.1 lateraloccipital 2844 1902 8104 3.459 0.720 0.146 0.068 388 7.9 lateralorbitofrontal 3271 2190 5882 2.272 0.690 0.164 0.091 77 10.5 lingual 1892 1280 5681 3.370 0.893 0.133 0.076 35 4.9 medialorbitofrontal 3406 2290 10572 3.227 0.820 0.152 0.075 70 9.7 middletemporal 770 491 2115 3.454 0.843 0.124 0.052 9 1.3 parahippocampal 2009 1262 4380 2.749 0.839 0.140 0.065 39 5.5 paracentral 1498 986 3874 2.999 0.672 0.141 0.059 30 3.4 parsopercularis 843 532 3205 4.254 0.605 0.159 0.089 16 2.8 parsorbitalis 1331 858 3380 2.982 0.761 0.146 0.069 29 4.4 parstriangularis 1454 975 1963 1.984 0.630 0.125 0.043 13 2.1 pericalcarine 5129 3367 9328 2.265 0.840 0.160 0.122 383 21.4 postcentral 963 642 1264 2.191 1.307 0.155 0.107 24 2.2 posteriorcingulate 5556 3753 11340 2.501 0.807 0.159 0.091 328 22.2 precentral 4264 2876 9938 2.644 1.091 0.174 0.325 348 25.5 precuneus 927 626 3174 4.121 0.664 0.156 0.071 20 3.3 rostralanteriorcingulate 5983 3864 15285 2.985 0.884 0.151 0.084 165 16.9 rostralmiddlefrontal 7401 4966 20600 3.069 1.114 0.165 0.112 313 33.9 superiorfrontal 6828 4802 14159 2.281 0.854 0.182 0.180 2893 38.2 superiorparietal 3394 2190 9195 3.264 0.762 0.138 0.061 69 9.0 superiortemporal 2817 1901 6828 2.664 1.134 0.176 0.162 221 23.9 supramarginal 224 157 1116 3.821 0.807 0.196 0.093 6 0.9 frontalpole 493 387 2605 4.048 0.635 0.170 0.064 10 1.4 temporalpole 454 279 1057 3.301 0.567 0.148 0.058 7 1.0 transversetemporal 2163 1452 5070 3.390 0.864 0.099 0.030 15 2.7 insula #----------------------------------------- #@# Cortical Parc 2 lh Fri Mar 18 18:16:55 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 Freesurfer lh ../surf/lh.sphere.reg /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/lh.destrieux.simple.2009-07-29.gcs ../label/lh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/lh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 3.9 0.2 using min determinant for regularization = 0.000 0 singular and 1066 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 15 labels changed using aseg relabeling using gibbs priors... 000: 6697 changed, 94903 examined... 001: 1518 changed, 26047 examined... 002: 451 changed, 7958 examined... 003: 151 changed, 2556 examined... 004: 87 changed, 895 examined... 005: 37 changed, 480 examined... 006: 19 changed, 195 examined... 007: 18 changed, 113 examined... 008: 9 changed, 94 examined... 009: 5 changed, 49 examined... 010: 4 changed, 30 examined... 011: 0 changed, 21 examined... 14 labels changed using aseg 000: 228 total segments, 145 labels (1435 vertices) changed 001: 88 total segments, 5 labels (17 vertices) changed 002: 83 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 111 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 488 vertices marked for relabeling... 488 labels changed in reclassification. writing output to ../label/lh.aparc.a2009s.annot... classification took 0 minutes and 41 seconds. #----------------------------------------- #@# Parcellation Stats 2 lh Fri Mar 18 18:17:35 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab Freesurfer lh white computing statistics for each annotation in ../label/lh.aparc.a2009s.annot. reading volume /tmp/surfaKCaG0free/MRI/Freesurfer/mri/wm.mgz... reading input surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white... reading input pial surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.pial... reading input white surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 620 423 1968 3.248 1.014 0.169 0.074 22 1.8 G_and_S_frontomargin 988 629 1978 2.658 0.651 0.159 0.063 18 2.4 G_and_S_occipital_inf 1295 817 2753 2.555 0.691 0.166 0.185 76 10.3 G_and_S_paracentral 996 662 3029 3.193 0.726 0.164 0.082 29 2.8 G_and_S_subcentral 467 320 1911 3.668 0.769 0.184 0.124 18 1.7 G_and_S_transv_frontopol 1492 1033 4687 3.783 0.801 0.155 0.067 28 4.6 G_and_S_cingul-Ant 751 520 1577 2.549 1.524 0.173 0.123 25 3.1 G_and_S_cingul-Mid-Ant 943 626 1649 2.176 0.979 0.196 0.129 107 3.4 G_and_S_cingul-Mid-Post 196 127 273 2.157 1.197 0.252 0.123 8 1.1 G_cingul-Post-dorsal 114 56 233 3.134 0.832 0.174 0.117 3 0.7 G_cingul-Post-ventral 1327 874 2655 2.433 0.610 0.195 0.115 38 5.8 G_cuneus 919 589 2923 3.367 0.581 0.168 0.079 27 2.8 G_front_inf-Opercular 216 129 806 3.660 0.805 0.178 0.102 10 1.3 G_front_inf-Orbital 803 486 2522 3.175 0.697 0.156 0.094 19 3.5 G_front_inf-Triangul 3903 2453 12486 3.278 1.006 0.169 0.099 121 15.6 G_front_middle 5376 3542 16551 3.245 1.080 0.164 0.115 193 27.2 G_front_sup 267 164 877 4.261 0.715 0.088 0.029 2 0.2 G_Ins_lg_and_S_cent_ins 373 236 1403 4.059 0.562 0.097 0.037 3 0.6 G_insular_short 1740 1123 4509 2.796 0.830 0.175 0.113 56 7.0 G_occipital_middle 1256 819 1800 1.839 0.672 0.179 0.117 44 4.9 G_occipital_sup 820 518 2255 3.255 0.599 0.151 0.071 17 2.6 G_oc-temp_lat-fusifor 2267 1463 4204 2.258 0.666 0.184 0.117 60 9.5 G_oc-temp_med-Lingual 827 525 2630 3.660 0.779 0.147 0.075 19 2.1 G_oc-temp_med-Parahip 1925 1264 7053 3.914 0.682 0.164 0.095 383 7.0 G_orbital 1025 599 2310 2.412 1.114 0.151 0.119 31 5.8 G_pariet_inf-Angular 1825 1183 5178 2.872 1.148 0.194 0.138 81 9.9 G_pariet_inf-Supramar 3028 2225 8773 2.781 0.817 0.171 0.094 76 9.3 G_parietal_sup 2224 1377 4056 2.188 0.741 0.173 0.094 97 7.1 G_postcentral 2049 1340 4972 2.746 0.742 0.160 0.075 65 5.9 G_precentral 2310 1568 6638 2.776 1.168 0.199 0.514 290 18.2 G_precuneus 721 486 3077 3.731 0.736 0.184 0.152 27 4.0 G_rectus 274 184 755 3.635 0.886 0.090 0.024 2 0.2 G_subcallosal 388 229 999 3.393 0.516 0.147 0.068 7 1.0 G_temp_sup-G_T_transv 1348 831 4842 3.574 0.608 0.164 0.077 37 4.5 G_temp_sup-Lateral 313 247 1027 3.657 0.500 0.112 0.024 2 0.3 G_temp_sup-Plan_polar 481 327 1081 2.796 0.614 0.100 0.021 2 0.4 G_temp_sup-Plan_tempo 2059 1403 7717 3.603 0.799 0.179 0.093 54 7.3 G_temporal_inf 2217 1475 7678 3.343 0.814 0.170 0.092 56 7.6 G_temporal_middle 240 162 581 2.989 0.736 0.137 0.031 3 0.3 Lat_Fis-ant-Horizont 158 101 271 2.231 0.574 0.093 0.020 1 0.1 Lat_Fis-ant-Vertical 889 613 1411 2.757 0.658 0.120 0.031 6 1.2 Lat_Fis-post 2294 1437 2649 1.719 0.512 0.160 0.086 52 9.0 Pole_occipital 1197 809 5229 3.989 0.722 0.162 0.077 25 3.8 Pole_temporal 1761 1221 2544 2.166 0.765 0.116 0.051 15 2.3 S_calcarine 2515 1808 3267 1.857 0.664 0.179 0.162 432 16.4 S_central 1152 747 1514 2.020 0.677 0.100 0.075 17 1.3 S_cingul-Marginalis 400 267 774 3.121 0.641 0.109 0.035 3 0.7 S_circular_insula_ant 1012 669 1865 3.250 0.753 0.092 0.022 5 1.0 S_circular_insula_inf 1219 860 2181 2.902 0.549 0.103 0.024 7 1.3 S_circular_insula_sup 706 492 1385 2.790 0.820 0.119 0.029 6 1.0 S_collat_transv_ant 274 186 434 2.493 0.620 0.132 0.042 2 0.5 S_collat_transv_post 1935 1279 3315 2.542 0.649 0.131 0.084 32 3.5 S_front_inf 910 616 1848 2.781 0.619 0.128 0.045 9 1.8 S_front_middle 1977 1340 3818 2.518 0.756 0.133 0.072 39 3.9 S_front_sup 21 14 36 1.601 0.759 0.175 0.030 0 0.0 S_interm_prim-Jensen 1854 1302 2471 1.878 0.776 0.252 0.663 3025 37.6 S_intrapariet_and_P_trans 995 658 1263 1.939 0.589 0.124 0.036 8 1.5 S_oc_middle_and_Lunatus 868 593 1207 1.799 0.567 0.150 0.088 21 2.8 S_oc_sup_and_transversal 782 523 1256 2.357 0.787 0.151 0.152 79 2.2 S_occipital_ant 411 269 846 3.162 0.678 0.125 0.050 4 0.8 S_oc-temp_lat 1307 911 2490 2.871 0.714 0.130 0.045 40 2.4 S_oc-temp_med_and_Lingual 286 202 822 3.222 0.879 0.157 0.063 4 0.7 S_orbital_lateral 460 311 1214 3.216 0.853 0.132 0.059 7 1.0 S_orbital_med-olfact 1092 737 2788 3.517 0.879 0.134 0.046 11 2.0 S_orbital-H_Shaped 898 590 1806 3.139 0.700 0.130 0.054 12 1.6 S_parieto_occipital 891 550 1907 4.044 0.697 0.124 0.032 11 1.0 S_pericallosal 2087 1452 2875 1.943 0.684 0.143 0.083 33 9.4 S_postcentral 1073 704 1475 2.077 0.736 0.171 0.224 59 5.8 S_precentral-inf-part 880 607 1431 2.450 0.559 0.103 0.028 5 1.1 S_precentral-sup-part 556 377 1185 3.016 0.906 0.116 0.033 5 0.6 S_suborbital 730 482 1253 1.777 0.953 0.205 0.213 52 6.8 S_subparietal 807 542 1634 3.055 0.744 0.128 0.037 7 1.2 S_temporal_inf 3462 2346 6809 2.745 0.623 0.128 0.069 42 6.2 S_temporal_sup 178 119 417 3.551 0.942 0.091 0.020 1 0.2 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 lh Fri Mar 18 18:17:45 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 Freesurfer lh ../surf/lh.sphere.reg /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/lh.DKTatlas40.gcs ../label/lh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/lh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.007 0 singular and 293 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 777 labels changed using aseg relabeling using gibbs priors... 000: 2061 changed, 94903 examined... 001: 458 changed, 8954 examined... 002: 119 changed, 2530 examined... 003: 43 changed, 695 examined... 004: 16 changed, 265 examined... 005: 7 changed, 97 examined... 006: 4 changed, 53 examined... 007: 4 changed, 25 examined... 008: 2 changed, 27 examined... 009: 2 changed, 16 examined... 010: 2 changed, 12 examined... 011: 2 changed, 10 examined... 012: 1 changed, 12 examined... 013: 0 changed, 7 examined... 108 labels changed using aseg 000: 61 total segments, 28 labels (277 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 35 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 363 vertices marked for relabeling... 363 labels changed in reclassification. writing output to ../label/lh.aparc.DKTatlas40.annot... classification took 0 minutes and 36 seconds. #----------------------------------------- #@# Parcellation Stats 3 lh Fri Mar 18 18:18:21 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_anatomical_stats -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas40.stats -b -a ../label/lh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab Freesurfer lh white computing statistics for each annotation in ../label/lh.aparc.DKTatlas40.annot. reading volume /tmp/surfaKCaG0free/MRI/Freesurfer/mri/wm.mgz... reading input surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white... reading input pial surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.pial... reading input white surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/lh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 803 514 2262 3.620 1.390 0.142 0.068 17 2.0 caudalanteriorcingulate 2975 1960 7504 2.760 1.131 0.175 0.167 112 14.3 caudalmiddlefrontal 1837 1215 3510 2.473 0.683 0.181 0.101 48 7.2 cuneus 334 222 1083 3.365 0.685 0.144 0.058 4 0.7 entorhinal 2262 1489 5352 3.159 0.683 0.142 0.061 60 6.0 fusiform 3436 2231 7173 2.498 0.953 0.158 0.123 161 19.4 inferiorparietal 3381 2311 11127 3.460 0.876 0.165 0.102 141 10.8 inferiortemporal 676 428 1371 3.189 1.151 0.165 0.071 15 1.9 isthmuscingulate 6284 4017 9406 2.079 0.718 0.157 0.080 137 19.8 lateraloccipital 2944 1990 8955 3.504 0.791 0.152 0.073 402 8.7 lateralorbitofrontal 3203 2143 5770 2.275 0.688 0.165 0.092 76 10.5 lingual 1565 1053 4990 3.393 0.905 0.147 0.090 35 5.0 medialorbitofrontal 4464 2993 12948 3.174 0.799 0.151 0.090 87 11.9 middletemporal 792 506 2150 3.428 0.838 0.123 0.052 10 1.3 parahippocampal 2196 1392 4871 2.759 0.831 0.139 0.067 43 5.6 paracentral 1253 832 3229 2.993 0.690 0.146 0.064 28 3.1 parsopercularis 854 553 2850 3.771 0.811 0.151 0.066 18 2.6 parsorbitalis 1772 1128 4232 2.893 0.755 0.134 0.060 26 4.8 parstriangularis 1477 991 1986 1.982 0.634 0.125 0.042 13 2.1 pericalcarine 5817 3826 10703 2.283 0.853 0.158 0.117 400 23.1 postcentral 1148 794 1491 2.106 1.277 0.190 0.143 109 3.5 posteriorcingulate 5598 3783 11432 2.516 0.808 0.160 0.091 328 22.5 precentral 4165 2832 9795 2.611 1.104 0.177 0.333 348 25.4 precuneus 1274 879 4312 3.998 0.700 0.151 0.067 25 3.9 rostralanteriorcingulate 4465 2858 11547 3.047 0.944 0.148 0.081 117 11.8 rostralmiddlefrontal 8219 5467 23013 3.112 1.035 0.158 0.104 253 35.6 superiorfrontal 5445 3876 11709 2.312 0.855 0.185 0.200 2848 33.2 superiorparietal 4576 3034 12957 3.275 0.773 0.136 0.055 83 11.0 superiortemporal 2903 1941 6760 2.607 1.140 0.182 0.240 267 25.5 supramarginal 463 283 1092 3.334 0.588 0.146 0.058 7 1.0 transversetemporal 1839 1228 4528 3.446 0.856 0.097 0.030 13 2.3 insula #-------------------------------------------- #@# Tessellate rh Fri Mar 18 18:18:29 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz Iteration Number : 1 pass 1 (xy+): 0 found - 0 modified | TOTAL: 0 pass 1 (xy-): 0 found - 0 modified | TOTAL: 0 pass 1 (yz+): 1 found - 1 modified | TOTAL: 1 pass 2 (yz+): 0 found - 1 modified | TOTAL: 1 pass 1 (yz-): 0 found - 0 modified | TOTAL: 1 pass 1 (xz+): 1 found - 1 modified | TOTAL: 2 pass 2 (xz+): 0 found - 1 modified | TOTAL: 2 pass 1 (xz-): 0 found - 0 modified | TOTAL: 2 Iteration Number : 1 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 pass 1 (+++): 0 found - 0 modified | TOTAL: 0 Iteration Number : 1 pass 1 (++): 0 found - 0 modified | TOTAL: 0 pass 1 (+-): 0 found - 0 modified | TOTAL: 0 pass 1 (--): 0 found - 0 modified | TOTAL: 0 pass 1 (-+): 0 found - 0 modified | TOTAL: 0 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 = 2 (out of 154247: 0.001297) Ambiguous edge configurations... mri_pretess done mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ slice 60: 1471 vertices, 1571 faces slice 70: 6127 vertices, 6315 faces slice 80: 12081 vertices, 12334 faces slice 90: 19589 vertices, 19912 faces slice 100: 28503 vertices, 28837 faces slice 110: 39075 vertices, 39465 faces slice 120: 50696 vertices, 51191 faces slice 130: 61980 vertices, 62476 faces slice 140: 73128 vertices, 73540 faces slice 150: 80862 vertices, 81181 faces slice 160: 88210 vertices, 88571 faces slice 170: 95101 vertices, 95436 faces slice 180: 100497 vertices, 100794 faces slice 190: 104738 vertices, 104956 faces slice 200: 105764 vertices, 105880 faces slice 210: 105764 vertices, 105880 faces slice 220: 105764 vertices, 105880 faces slice 230: 105764 vertices, 105880 faces slice 240: 105764 vertices, 105880 faces slice 250: 105764 vertices, 105880 faces using the conformed surface RAS to save vertex points... writing ../surf/rh.orig.nofix using vox2ras matrix: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; rm -f ../mri/filled-pretess127.mgz mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix counting number of connected components... 105764 voxel in cpt #1: X=-116 [v=105764,e=317640,f=211760] located at (24.602493, -6.011932, 27.141787) For the whole surface: X=-116 [v=105764,e=317640,f=211760] One single component has been found nothing to do done #-------------------------------------------- #@# Smooth1 rh Fri Mar 18 18:18:35 EDT 2016 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix /tmp/surfaKCaG0free/MRI/Freesurfer/scripts setting seed for random number generator to 1234 smoothing surface tessellation for 10 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation1 rh Fri Mar 18 18:18:38 EDT 2016 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix /tmp/surfaKCaG0free/MRI/Freesurfer/scripts avg radius = 40.1 mm, total surface area = 54428 mm^2 writing inflated surface to ../surf/rh.inflated.nofix inflation took 0.4 minutes Not saving sulc step 000: RMS=0.116 (target=0.015) step 005: RMS=0.090 (target=0.015) step 010: RMS=0.073 (target=0.015) step 015: RMS=0.065 (target=0.015) step 020: RMS=0.061 (target=0.015) step 025: RMS=0.057 (target=0.015) step 030: RMS=0.056 (target=0.015) step 035: RMS=0.053 (target=0.015) step 040: RMS=0.051 (target=0.015) step 045: RMS=0.051 (target=0.015) step 050: RMS=0.050 (target=0.015) step 055: RMS=0.050 (target=0.015) step 060: RMS=0.049 (target=0.015) inflation complete. Not saving sulc #-------------------------------------------- #@# QSphere rh Fri Mar 18 18:19:00 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix doing quick spherical unfolding. setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... vertex spacing 1.06 +- 0.75 (0.00-->10.62) (max @ vno 72446 --> 72447) face area 0.03 +- 0.05 (-0.64-->1.80) scaling brain by 0.355... inflating to sphere (rms error < 2.00) 000: dt: 0.0000, rms radial error=177.281, avgs=0 005/300: dt: 0.9000, rms radial error=177.020, avgs=0 010/300: dt: 0.9000, rms radial error=176.460, avgs=0 015/300: dt: 0.9000, rms radial error=175.725, avgs=0 020/300: dt: 0.9000, rms radial error=174.887, avgs=0 025/300: dt: 0.9000, rms radial error=173.992, avgs=0 030/300: dt: 0.9000, rms radial error=173.064, avgs=0 035/300: dt: 0.9000, rms radial error=172.119, avgs=0 040/300: dt: 0.9000, rms radial error=171.167, avgs=0 045/300: dt: 0.9000, rms radial error=170.213, avgs=0 050/300: dt: 0.9000, rms radial error=169.258, avgs=0 055/300: dt: 0.9000, rms radial error=168.306, avgs=0 060/300: dt: 0.9000, rms radial error=167.358, avgs=0 065/300: dt: 0.9000, rms radial error=166.414, avgs=0 070/300: dt: 0.9000, rms radial error=165.474, avgs=0 075/300: dt: 0.9000, rms radial error=164.538, avgs=0 080/300: dt: 0.9000, rms radial error=163.608, avgs=0 085/300: dt: 0.9000, rms radial error=162.683, avgs=0 090/300: dt: 0.9000, rms radial error=161.762, avgs=0 095/300: dt: 0.9000, rms radial error=160.847, avgs=0 100/300: dt: 0.9000, rms radial error=159.936, avgs=0 105/300: dt: 0.9000, rms radial error=159.030, avgs=0 110/300: dt: 0.9000, rms radial error=158.130, avgs=0 115/300: dt: 0.9000, rms radial error=157.234, avgs=0 120/300: dt: 0.9000, rms radial error=156.343, avgs=0 125/300: dt: 0.9000, rms radial error=155.458, avgs=0 130/300: dt: 0.9000, rms radial error=154.577, avgs=0 135/300: dt: 0.9000, rms radial error=153.701, avgs=0 140/300: dt: 0.9000, rms radial error=152.829, avgs=0 145/300: dt: 0.9000, rms radial error=151.963, avgs=0 150/300: dt: 0.9000, rms radial error=151.102, avgs=0 155/300: dt: 0.9000, rms radial error=150.245, avgs=0 160/300: dt: 0.9000, rms radial error=149.393, avgs=0 165/300: dt: 0.9000, rms radial error=148.546, avgs=0 170/300: dt: 0.9000, rms radial error=147.704, avgs=0 175/300: dt: 0.9000, rms radial error=146.866, avgs=0 180/300: dt: 0.9000, rms radial error=146.033, avgs=0 185/300: dt: 0.9000, rms radial error=145.205, avgs=0 190/300: dt: 0.9000, rms radial error=144.382, avgs=0 195/300: dt: 0.9000, rms radial error=143.564, avgs=0 200/300: dt: 0.9000, rms radial error=142.751, avgs=0 205/300: dt: 0.9000, rms radial error=141.943, avgs=0 210/300: dt: 0.9000, rms radial error=141.140, avgs=0 215/300: dt: 0.9000, rms radial error=140.341, avgs=0 220/300: dt: 0.9000, rms radial error=139.547, avgs=0 225/300: dt: 0.9000, rms radial error=138.757, avgs=0 230/300: dt: 0.9000, rms radial error=137.971, avgs=0 235/300: dt: 0.9000, rms radial error=137.190, avgs=0 240/300: dt: 0.9000, rms radial error=136.413, avgs=0 245/300: dt: 0.9000, rms radial error=135.641, avgs=0 250/300: dt: 0.9000, rms radial error=134.873, avgs=0 255/300: dt: 0.9000, rms radial error=134.109, avgs=0 260/300: dt: 0.9000, rms radial error=133.350, avgs=0 265/300: dt: 0.9000, rms radial error=132.595, avgs=0 270/300: dt: 0.9000, rms radial error=131.844, avgs=0 275/300: dt: 0.9000, rms radial error=131.098, avgs=0 280/300: dt: 0.9000, rms radial error=130.355, avgs=0 285/300: dt: 0.9000, rms radial error=129.617, avgs=0 290/300: dt: 0.9000, rms radial error=128.883, avgs=0 295/300: dt: 0.9000, rms radial error=128.153, avgs=0 300/300: dt: 0.9000, rms radial error=127.428, avgs=0 spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 12062.63 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 = 2039.06 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.00/10 = 0.00024 epoch 3 (K=160.0), pass 1, starting sse = 253.65 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.03/10 = 0.00282 epoch 4 (K=640.0), pass 1, starting sse = 35.44 taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.04/10 = 0.00385 final writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.05 hours distance error %100000.00 #-------------------------------------------- #@# Fix Topology rh Fri Mar 18 18:21:42 EDT 2016 cp ../surf/rh.orig.nofix ../surf/rh.orig cp ../surf/rh.inflated.nofix ../surf/rh.inflated /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234 Freesurfer rh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters setting seed for random number genererator to 1234 ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ before topology correction, eno=-116 (nv=105764, nf=211760, ne=317640, g=59) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 10 iterations marking ambiguous vertices... 18000 ambiguous faces found in tessellation segmenting defects... 63 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 2 into 0 -merging segment 23 into 5 -merging segment 5 into 9 -merging segment 9 into 10 59 defects to be corrected 0 vertices coincident reading input surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2054 (-4.6027) -vertex loglikelihood: -6.2778 (-3.1389) -normal dot loglikelihood: -3.4886 (-3.4886) -quad curv loglikelihood: -6.4109 (-3.2054) Total Loglikelihood : -25.3827 CORRECTING DEFECT 0 (vertices=242, convex hull=204) After retessellation of defect 0, euler #=-55 (95664,284562,188843) : difference with theory (-56) = -1 CORRECTING DEFECT 1 (vertices=267, convex hull=185) After retessellation of defect 1, euler #=-54 (95718,284811,189039) : difference with theory (-55) = -1 CORRECTING DEFECT 2 (vertices=121, convex hull=113) After retessellation of defect 2, euler #=-53 (95764,284996,189179) : difference with theory (-54) = -1 CORRECTING DEFECT 3 (vertices=49, convex hull=80) After retessellation of defect 3, euler #=-52 (95779,285069,189238) : difference with theory (-53) = -1 CORRECTING DEFECT 4 (vertices=8, convex hull=29) After retessellation of defect 4, euler #=-51 (95780,285081,189250) : difference with theory (-52) = -1 CORRECTING DEFECT 5 (vertices=255, convex hull=204) After retessellation of defect 5, euler #=-50 (95861,285425,189514) : difference with theory (-51) = -1 CORRECTING DEFECT 6 (vertices=61, convex hull=46) After retessellation of defect 6, euler #=-49 (95870,285471,189552) : difference with theory (-50) = -1 CORRECTING DEFECT 7 (vertices=1926, convex hull=509) After retessellation of defect 7, euler #=-46 (96207,286750,190497) : difference with theory (-49) = -3 CORRECTING DEFECT 8 (vertices=47, convex hull=101) After retessellation of defect 8, euler #=-45 (96221,286829,190563) : difference with theory (-48) = -3 CORRECTING DEFECT 9 (vertices=44, convex hull=52) After retessellation of defect 9, euler #=-44 (96232,286876,190600) : difference with theory (-47) = -3 CORRECTING DEFECT 10 (vertices=26, convex hull=22) After retessellation of defect 10, euler #=-43 (96232,286883,190608) : difference with theory (-46) = -3 CORRECTING DEFECT 11 (vertices=100, convex hull=93) After retessellation of defect 11, euler #=-42 (96272,287045,190731) : difference with theory (-45) = -3 CORRECTING DEFECT 12 (vertices=57, convex hull=45) After retessellation of defect 12, euler #=-41 (96280,287086,190765) : difference with theory (-44) = -3 CORRECTING DEFECT 13 (vertices=20, convex hull=65) After retessellation of defect 13, euler #=-40 (96292,287145,190813) : difference with theory (-43) = -3 CORRECTING DEFECT 14 (vertices=26, convex hull=81) After retessellation of defect 14, euler #=-39 (96301,287208,190868) : difference with theory (-42) = -3 CORRECTING DEFECT 15 (vertices=2766, convex hull=359) After retessellation of defect 15, euler #=-39 (96992,289464,192433) : difference with theory (-41) = -2 CORRECTING DEFECT 16 (vertices=19, convex hull=56) After retessellation of defect 16, euler #=-38 (97001,289514,192475) : difference with theory (-40) = -2 CORRECTING DEFECT 17 (vertices=62, convex hull=85) After retessellation of defect 17, euler #=-37 (97024,289616,192555) : difference with theory (-39) = -2 CORRECTING DEFECT 18 (vertices=27, convex hull=45) After retessellation of defect 18, euler #=-36 (97031,289654,192587) : difference with theory (-38) = -2 CORRECTING DEFECT 19 (vertices=6, convex hull=19) After retessellation of defect 19, euler #=-35 (97032,289661,192594) : difference with theory (-37) = -2 CORRECTING DEFECT 20 (vertices=255, convex hull=111) After retessellation of defect 20, euler #=-35 (97082,289868,192751) : difference with theory (-36) = -1 CORRECTING DEFECT 21 (vertices=210, convex hull=170) After retessellation of defect 21, euler #=-34 (97137,290110,192939) : difference with theory (-35) = -1 CORRECTING DEFECT 22 (vertices=223, convex hull=127) After retessellation of defect 22, euler #=-34 (97167,290281,193080) : difference with theory (-34) = 0 CORRECTING DEFECT 23 (vertices=24, convex hull=59) After retessellation of defect 23, euler #=-33 (97179,290340,193128) : difference with theory (-33) = 0 CORRECTING DEFECT 24 (vertices=23, convex hull=29) After retessellation of defect 24, euler #=-32 (97181,290354,193141) : difference with theory (-32) = 0 CORRECTING DEFECT 25 (vertices=32, convex hull=84) After retessellation of defect 25, euler #=-31 (97201,290449,193217) : difference with theory (-31) = 0 CORRECTING DEFECT 26 (vertices=52, convex hull=32) After retessellation of defect 26, euler #=-30 (97209,290481,193242) : difference with theory (-30) = 0 CORRECTING DEFECT 27 (vertices=28, convex hull=60) After retessellation of defect 27, euler #=-29 (97224,290550,193297) : difference with theory (-29) = 0 CORRECTING DEFECT 28 (vertices=24, convex hull=60) After retessellation of defect 28, euler #=-28 (97236,290608,193344) : difference with theory (-28) = 0 CORRECTING DEFECT 29 (vertices=121, convex hull=120) After retessellation of defect 29, euler #=-27 (97280,290798,193491) : difference with theory (-27) = 0 CORRECTING DEFECT 30 (vertices=30, convex hull=30) After retessellation of defect 30, euler #=-26 (97284,290820,193510) : difference with theory (-26) = 0 CORRECTING DEFECT 31 (vertices=53, convex hull=110) After retessellation of defect 31, euler #=-25 (97302,290924,193597) : difference with theory (-25) = 0 CORRECTING DEFECT 32 (vertices=374, convex hull=105) After retessellation of defect 32, euler #=-24 (97355,291134,193755) : difference with theory (-24) = 0 CORRECTING DEFECT 33 (vertices=67, convex hull=95) After retessellation of defect 33, euler #=-23 (97369,291213,193821) : difference with theory (-23) = 0 CORRECTING DEFECT 34 (vertices=78, convex hull=43) After retessellation of defect 34, euler #=-22 (97380,291261,193859) : difference with theory (-22) = 0 CORRECTING DEFECT 35 (vertices=24, convex hull=42) After retessellation of defect 35, euler #=-21 (97390,291308,193897) : difference with theory (-21) = 0 CORRECTING DEFECT 36 (vertices=6, convex hull=23) After retessellation of defect 36, euler #=-20 (97392,291320,193908) : difference with theory (-20) = 0 CORRECTING DEFECT 37 (vertices=293, convex hull=74) After retessellation of defect 37, euler #=-19 (97423,291450,194008) : difference with theory (-19) = 0 CORRECTING DEFECT 38 (vertices=6, convex hull=27) After retessellation of defect 38, euler #=-18 (97424,291460,194018) : difference with theory (-18) = 0 CORRECTING DEFECT 39 (vertices=464, convex hull=545) After retessellation of defect 39, euler #=-17 (97624,292326,194685) : difference with theory (-17) = 0 CORRECTING DEFECT 40 (vertices=5, convex hull=13) Warning - incorrect dp selected!!!!(-165.938889 >= -165.938897 ) After retessellation of defect 40, euler #=-16 (97625,292332,194691) : difference with theory (-16) = 0 CORRECTING DEFECT 41 (vertices=31, convex hull=47) After retessellation of defect 41, euler #=-15 (97629,292361,194717) : difference with theory (-15) = 0 CORRECTING DEFECT 42 (vertices=181, convex hull=94) After retessellation of defect 42, euler #=-14 (97674,292543,194855) : difference with theory (-14) = 0 CORRECTING DEFECT 43 (vertices=21, convex hull=61) After retessellation of defect 43, euler #=-13 (97683,292593,194897) : difference with theory (-13) = 0 CORRECTING DEFECT 44 (vertices=15, convex hull=24) After retessellation of defect 44, euler #=-12 (97686,292607,194909) : difference with theory (-12) = 0 CORRECTING DEFECT 45 (vertices=8, convex hull=29) After retessellation of defect 45, euler #=-11 (97688,292621,194922) : difference with theory (-11) = 0 CORRECTING DEFECT 46 (vertices=36, convex hull=49) After retessellation of defect 46, euler #=-10 (97709,292704,194985) : difference with theory (-10) = 0 CORRECTING DEFECT 47 (vertices=82, convex hull=91) After retessellation of defect 47, euler #=-9 (97722,292791,195060) : difference with theory (-9) = 0 CORRECTING DEFECT 48 (vertices=486, convex hull=201) After retessellation of defect 48, euler #=-8 (97747,292965,195210) : difference with theory (-8) = 0 CORRECTING DEFECT 49 (vertices=19, convex hull=20) After retessellation of defect 49, euler #=-7 (97747,292970,195216) : difference with theory (-7) = 0 CORRECTING DEFECT 50 (vertices=127, convex hull=59) After retessellation of defect 50, euler #=-6 (97760,293032,195266) : difference with theory (-6) = 0 CORRECTING DEFECT 51 (vertices=340, convex hull=114) normal vector of length zero at vertex 105125 with 4 faces normal vector of length zero at vertex 105125 with 4 faces normal vector of length zero at vertex 105125 with 4 faces normal vector of length zero at vertex 105125 with 4 faces normal vector of length zero at vertex 105125 with 4 faces normal vector of length zero at vertex 105125 with 4 faces After retessellation of defect 51, euler #=-5 (97769,293108,195334) : difference with theory (-5) = 0 CORRECTING DEFECT 52 (vertices=10, convex hull=37) After retessellation of defect 52, euler #=-4 (97770,293121,195347) : difference with theory (-4) = 0 CORRECTING DEFECT 53 (vertices=25, convex hull=64) After retessellation of defect 53, euler #=-3 (97787,293195,195405) : difference with theory (-3) = 0 CORRECTING DEFECT 54 (vertices=110, convex hull=128) After retessellation of defect 54, euler #=-2 (97833,293393,195558) : difference with theory (-2) = 0 CORRECTING DEFECT 55 (vertices=58, convex hull=92) After retessellation of defect 55, euler #=-1 (97855,293499,195643) : difference with theory (-1) = 0 CORRECTING DEFECT 56 (vertices=14, convex hull=22) After retessellation of defect 56, euler #=0 (97857,293513,195656) : difference with theory (0) = 0 CORRECTING DEFECT 57 (vertices=69, convex hull=101) After retessellation of defect 57, euler #=1 (97883,293634,195752) : difference with theory (1) = 0 CORRECTING DEFECT 58 (vertices=22, convex hull=18) After retessellation of defect 58, euler #=2 (97884,293646,195764) : difference with theory (2) = 0 computing original vertex metric properties... storing new metric properties... computing tessellation statistics... vertex spacing 0.89 +- 0.31 (0.04-->15.68) (max @ vno 36566 --> 101242) face area 0.00 +- 0.00 (0.00-->0.00) performing soap bubble on retessellated vertices for 0 iterations... vertex spacing 0.89 +- 0.31 (0.04-->15.68) (max @ vno 36566 --> 101242) face area 0.00 +- 0.00 (0.00-->0.00) tessellation finished, orienting corrected surface... 224 mutations (35.1%), 415 crossovers (64.9%), 396 vertices were eliminated building final representation... 7880 vertices and 0 faces have been removed from triangulation after topology correction, eno=2 (nv=97884, nf=195764, ne=293646, g=0) writing corrected surface to /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.orig... 0.000 % of the vertices (0 vertices) exhibit an orientation change topology fixing took 49.6 minutes 0 defective edges removing intersecting faces 000: 1340 intersecting 001: 274 intersecting 002: 186 intersecting 003: 121 intersecting 004: 76 intersecting 005: 41 intersecting 006: 29 intersecting expanding nbhd size to 2 007: 36 intersecting expanding nbhd size to 3 008: 41 intersecting 009: 36 intersecting 010: 34 intersecting 011: 25 intersecting expanding nbhd size to 4 012: 26 intersecting expanding nbhd size to 5 013: 33 intersecting 014: 27 intersecting 015: 19 intersecting 016: 14 intersecting 017: 10 intersecting 018: 7 intersecting 019: 5 intersecting mris_euler_number ../surf/rh.orig euler # = v-e+f = 2g-2: 97884 - 293646 + 195764 = 2 --> 0 holes F =2V-4: 195764 = 195768-4 (0) 2E=3F: 587292 = 587292 (0) total defect index = 0 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_remove_intersection ../surf/rh.orig ../surf/rh.orig intersection removal took 0.00 hours removing intersecting faces 000: 763 intersecting 001: 239 intersecting 002: 186 intersecting 003: 120 intersecting 004: 76 intersecting 005: 36 intersecting 006: 21 intersecting expanding nbhd size to 2 007: 54 intersecting 008: 22 intersecting expanding nbhd size to 3 009: 38 intersecting 010: 28 intersecting 011: 20 intersecting 012: 18 intersecting expanding nbhd size to 4 013: 27 intersecting 014: 14 intersecting expanding nbhd size to 5 015: 17 intersecting 016: 12 intersecting expanding nbhd size to 6 017: 15 intersecting 018: 10 intersecting expanding nbhd size to 7 019: 12 intersecting 020: 5 intersecting writing corrected surface to ../surf/rh.orig rm ../surf/rh.inflated #-------------------------------------------- #@# Make White Surf rh Fri Mar 18 19:11:33 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_make_surfaces -noaparc -whiteonly -mgz -T1 brain.finalsurfs Freesurfer rh only generating white matter surface not using aparc to prevent surfaces crossing the midline INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /tmp/surfaKCaG0free/MRI/Freesurfer/mri/filled.mgz... reading volume /tmp/surfaKCaG0free/MRI/Freesurfer/mri/brain.finalsurfs.mgz... reading volume /tmp/surfaKCaG0free/MRI/Freesurfer/mri/wm.mgz... 10109 bright wm thresholded. 4486 bright non-wm voxels segmented. reading original surface position from /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.orig... computing class statistics... border white: 173912 voxels (1.04%) border gray 218602 voxels (1.30%) WM (94.0): 95.6 +- 8.0 [70.0 --> 110.0] GM (84.0) : 82.6 +- 10.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 65.7 (was 70) setting MAX_BORDER_WHITE to 112.0 (was 105) setting MIN_BORDER_WHITE to 76.0 (was 85) setting MAX_CSF to 55.4 (was 40) setting MAX_GRAY to 96.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 70.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 45.1 (was 40) repositioning cortical surface to gray/white boundary reading volume /tmp/surfaKCaG0free/MRI/Freesurfer/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.25 (0.01-->7.54) (max @ vno 79283 --> 87452) face area 0.28 +- 0.15 (0.00-->6.90) mean absolute distance = 0.71 +- 0.92 3001 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=104, GM=76 mean inside = 95.2, mean outside = 80.9 smoothing surface for 5 iterations... inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=85.3, 320 (320) missing vertices, mean dist 0.2 [0.7 (%36.9)->0.7 (%63.1))] %69 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=rc-ru, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.30 (0.08-->7.57) (max @ vno 79283 --> 87452) face area 0.28 +- 0.16 (0.00-->6.00) mean absolute distance = 0.38 +- 0.59 2224 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5612789.0, rms=13.58 001: dt: 0.5000, sse=5559630.0, rms=10.963 (0.000%) 002: dt: 0.5000, sse=5377745.0, rms=8.971 (0.000%) 003: dt: 0.5000, sse=5301182.0, rms=7.599 (0.000%) 004: dt: 0.5000, sse=5241556.5, rms=6.559 (0.000%) 005: dt: 0.5000, sse=5180311.5, rms=5.775 (0.000%) 006: dt: 0.5000, sse=5175613.0, rms=5.283 (0.000%) 007: dt: 0.5000, sse=5195216.5, rms=4.978 (0.000%) 008: dt: 0.5000, sse=5206026.5, rms=4.820 (0.000%) 009: dt: 0.5000, sse=5180747.5, rms=4.708 (0.000%) 010: dt: 0.5000, sse=5216669.0, rms=4.626 (0.000%) rms = 4.59, time step reduction 1 of 3 to 0.250... 011: dt: 0.5000, sse=5192939.5, rms=4.586 (0.000%) 012: dt: 0.2500, sse=3516489.8, rms=4.078 (0.000%) 013: dt: 0.2500, sse=3356400.2, rms=3.981 (0.000%) rms = 3.97, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=3285060.8, rms=3.974 (0.000%) 015: dt: 0.1250, sse=3211998.8, rms=3.858 (0.000%) rms = 3.82, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=3185959.0, rms=3.822 (0.000%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 4 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group mean border=88.0, 238 (59) missing vertices, mean dist -0.2 [0.4 (%75.6)->0.3 (%24.4))] %80 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=rc-ru, 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 +- 0.29 (0.09-->7.67) (max @ vno 96845 --> 35664) face area 0.34 +- 0.20 (0.00-->7.68) mean absolute distance = 0.27 +- 0.41 2343 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3347112.5, rms=4.64 017: dt: 0.5000, sse=3736052.8, rms=3.540 (0.000%) 018: dt: 0.5000, sse=3873611.8, rms=3.339 (0.000%) rms = 3.33, time step reduction 1 of 3 to 0.250... 019: dt: 0.5000, sse=4132163.0, rms=3.333 (0.000%) 020: dt: 0.2500, sse=3480814.0, rms=2.812 (0.000%) 021: dt: 0.2500, sse=3371386.5, rms=2.748 (0.000%) rms = 2.73, time step reduction 2 of 3 to 0.125... 022: dt: 0.2500, sse=3304611.2, rms=2.734 (0.000%) 023: dt: 0.1250, sse=3256394.0, rms=2.626 (0.000%) 024: dt: 0.1250, sse=3232262.0, rms=2.573 (0.000%) rms = 2.56, time step reduction 3 of 3 to 0.062... 025: dt: 0.1250, sse=3218196.5, rms=2.558 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=89.7, 291 (37) missing vertices, mean dist -0.1 [0.3 (%67.5)->0.3 (%32.5))] %84 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=rc-ru, 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 +- 0.29 (0.07-->8.00) (max @ vno 96845 --> 35664) face area 0.33 +- 0.20 (0.00-->7.22) mean absolute distance = 0.24 +- 0.34 2400 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3249767.8, rms=3.14 026: dt: 0.5000, sse=3682839.8, rms=3.046 (0.000%) 027: dt: 0.5000, sse=3718691.8, rms=2.838 (0.000%) rms = 3.08, time step reduction 1 of 3 to 0.250... 028: dt: 0.2500, sse=3420821.0, rms=2.389 (0.000%) 029: dt: 0.2500, sse=3375765.8, rms=2.287 (0.000%) rms = 2.31, time step reduction 2 of 3 to 0.125... 030: dt: 0.1250, sse=3332600.5, rms=2.218 (0.000%) 031: dt: 0.1250, sse=3294506.2, rms=2.136 (0.000%) rms = 2.11, time step reduction 3 of 3 to 0.062... 032: dt: 0.1250, sse=3280989.2, rms=2.108 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... removing 2 vertex label from ripped group removing 2 vertex label from ripped group removing 1 vertex label from ripped group removing 1 vertex label from ripped group removing 3 vertex label from ripped group removing 1 vertex label from ripped group removing 2 vertex label from ripped group mean border=90.1, 340 (32) missing vertices, mean dist -0.0 [0.2 (%54.1)->0.2 (%45.9))] %86 local maxima, % 5 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=rc-ru, 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 /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white... writing smoothed curvature to rh.curv 000: dt: 0.0000, sse=3295431.5, rms=2.40 rms = 2.91, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=3365108.2, rms=2.054 (0.000%) rms = 2.23, time step reduction 2 of 3 to 0.125... 034: dt: 0.1250, sse=3375042.5, rms=1.985 (0.000%) 035: dt: 0.1250, sse=3456861.8, rms=1.878 (0.000%) rms = 1.85, time step reduction 3 of 3 to 0.062... 036: dt: 0.1250, sse=3526808.0, rms=1.847 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group generating cortex label... 17 non-cortical segments detected only using segment with 1532 vertices erasing segment 1 (vno[0] = 30429) erasing segment 2 (vno[0] = 31555) erasing segment 3 (vno[0] = 34237) erasing segment 4 (vno[0] = 50879) erasing segment 5 (vno[0] = 58599) erasing segment 6 (vno[0] = 59741) erasing segment 7 (vno[0] = 59759) erasing segment 8 (vno[0] = 60783) erasing segment 9 (vno[0] = 63949) erasing segment 10 (vno[0] = 64902) erasing segment 11 (vno[0] = 65790) erasing segment 12 (vno[0] = 69490) erasing segment 13 (vno[0] = 70201) erasing segment 14 (vno[0] = 70796) erasing segment 15 (vno[0] = 72009) erasing segment 16 (vno[0] = 72017) writing cortex label to /tmp/surfaKCaG0free/MRI/Freesurfer/label/rh.cortex.label... writing curvature file /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.curv writing smoothed area to rh.area writing curvature file /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.area vertex spacing 0.89 +- 0.30 (0.04-->8.10) (max @ vno 35664 --> 96845) face area 0.33 +- 0.20 (0.00-->7.30) refinement took 4.2 minutes #-------------------------------------------- #@# Smooth2 rh Fri Mar 18 19:15:42 EDT 2016 mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white ../surf/rh.smoothwm /tmp/surfaKCaG0free/MRI/Freesurfer/scripts smoothing for 3 iterations setting seed for random number generator to 1234 smoothing surface tessellation for 3 iterations... smoothing complete - recomputing first and second fundamental forms... #-------------------------------------------- #@# Inflation2 rh Fri Mar 18 19:15:45 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated avg radius = 39.8 mm, total surface area = 58346 mm^2 writing inflated surface to ../surf/rh.inflated writing sulcal depths to ../surf/rh.sulc step 000: RMS=0.124 (target=0.015) step 005: RMS=0.090 (target=0.015) step 010: RMS=0.071 (target=0.015) step 015: RMS=0.060 (target=0.015) step 020: RMS=0.052 (target=0.015) step 025: RMS=0.046 (target=0.015) step 030: RMS=0.041 (target=0.015) step 035: RMS=0.035 (target=0.015) step 040: RMS=0.032 (target=0.015) step 045: RMS=0.029 (target=0.015) step 050: RMS=0.027 (target=0.015) step 055: RMS=0.025 (target=0.015) step 060: RMS=0.023 (target=0.015) inflation complete. inflation took 0.4 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/rh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 104 vertices thresholded to be in k1 ~ [-0.77 2.17], k2 ~ [-0.40 0.27] total integrated curvature = -0.252*4pi (-3.167) --> 1 handles ICI = 1.6, FI = 8.7, variation=175.882 95 vertices thresholded to be in [-0.26 0.10] writing Gaussian curvature to ../surf/rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.006 85 vertices thresholded to be in [-0.39 0.57] done. writing mean curvature to ../surf/rh.inflated.H...curvature mean = -0.024, std = 0.033 done. #----------------------------------------- #@# Curvature Stats rh Fri Mar 18 19:17:10 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/surf mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm Freesurfer rh curv sulc Toggling save flag on curvature files [ ok ] Outputting results using filestem [ ../stats/rh.curv.stats ] Toggling save flag on curvature files [ ok ] Setting surface [ Freesurfer/rh.smoothwm ] Reading surface... [ ok ] Setting texture [ curv ] Reading texture... [ ok ] Setting texture [ sulc ] Reading texture...Gb_filter = 0 [ ok ] Calculating Discrete Principal Curvatures... Determining geometric order for vertex faces... [####################] [ ok ] Determining KH curvatures... [####################] [ ok ] Determining k1k2 curvatures... [####################] [ ok ] deltaViolations [ 179 ] Gb_filter = 0 WARN: S lookup min: -0.242077 WARN: S explicit min: 0.000000 vertex = 507 #-------------------------------------------- #@# Sphere rh Fri Mar 18 19:17:12 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_sphere -seed 1234 ../surf/rh.inflated ../surf/rh.sphere setting seed for random number genererator to 1234 $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading original vertex positions... unfolding cortex into spherical form... surface projected - minimizing metric distortion... scaling brain by 0.336... MRISunfold() max_passes = 1 ------- tol=5.0e-01, sigma=0.0, host=rc-ru, nav=1024, nbrs=2, l_area=1.000, l_dist=1.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 1.000000 desired_rms_height -1.000000 momentum 0.900000 nbhd_size 7 max_nbrs 8 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 1234 -------------------- mrisRemoveNegativeArea() pass 1: epoch 1 of 3 starting distance error %44.94 pass 1: epoch 2 of 3 starting distance error %25.56 unfolding complete - removing small folds... starting distance error %24.77 removing remaining folds... final distance error %24.80 MRISunfold() return, current seed 1234 writing spherical brain to ../surf/rh.sphere spherical transformation took 0.48 hours #-------------------------------------------- #@# Surf Reg rh Fri Mar 18 19:45:51 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_register -curv ../surf/rh.sphere /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/rh.average.curvature.filled.buckner40.tif ../surf/rh.sphere.reg using smoothwm curvature for final alignment $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from ../surf/rh.sphere... reading template parameterization from /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/rh.average.curvature.filled.buckner40.tif... MRISregister() ------- max_passes = 4 min_degrees = 0.500000 max_degrees = 64.000000 nangles = 8 tol=5.0e-01, sigma=0.0, host=rc-ru, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height -1.000000 momentum 0.950000 nbhd_size -10 max_nbrs 10 niterations 25 nsurfaces 0 SURFACES 3 flags 16 (10) use curv 16 no sulc 0 no rigid align 0 mris->nsize 1 mris->hemisphere 1 randomSeed 0 tol=5.0e-01, sigma=0.0, host=rc-ru, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=1.000, l_dist=5.000 using quadratic fit line minimization -------------------- 1 Reading rh.sulc curvature mean = 0.000, std = 0.588 curvature mean = 0.021, std = 0.937 curvature mean = 0.026, std = 0.878 Starting MRISrigidBodyAlignGlobal() d=64.00 min @ (16.00, 0.00, 32.00) sse = 263953.8, tmin=0.6443 d=32.00 min @ (-8.00, 0.00, 0.00) sse = 232179.0, tmin=1.2848 d=16.00 min @ (-4.00, -4.00, -4.00) sse = 199839.4, tmin=1.9333 d=4.00 min @ (1.00, 0.00, 1.00) sse = 199383.6, tmin=3.3656 d=2.00 min @ (0.00, 0.50, -0.50) sse = 199147.0, tmin=4.0798 d=1.00 min @ (-0.25, -0.25, 0.00) sse = 199044.1, tmin=4.7626 d=0.50 min @ (0.00, 0.00, 0.12) sse = 199021.2, tmin=5.5168 tol=1.0e+00, sigma=0.5, host=rc-ru, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.000, l_corr=0.050, l_spring=0.500, l_dist=5.000 using quadratic fit line minimization MRISrigidBodyAlignGlobal() done 5.52 min curvature mean = -0.027, std = 0.975 curvature mean = 0.010, std = 0.950 curvature mean = -0.040, std = 0.979 curvature mean = 0.004, std = 0.977 curvature mean = -0.040, std = 0.981 curvature mean = 0.001, std = 0.989 2 Reading smoothwm curvature mean = -0.056, std = 0.362 curvature mean = 0.003, std = 0.071 curvature mean = 0.081, std = 0.328 curvature mean = 0.001, std = 0.087 curvature mean = 0.053, std = 0.482 curvature mean = 0.001, std = 0.094 curvature mean = 0.033, std = 0.604 curvature mean = 0.001, std = 0.097 curvature mean = 0.013, std = 0.721 MRISregister() return, current seed 0 writing registered surface to ../surf/rh.sphere.reg... expanding nbhd size to 1 #-------------------------------------------- #@# Jacobian white rh Fri Mar 18 20:03:54 EDT 2016 mris_jacobian ../surf/rh.white ../surf/rh.sphere.reg ../surf/rh.jacobian_white reading surface from ../surf/rh.white... writing curvature file ../surf/rh.jacobian_white #-------------------------------------------- #@# AvgCurv rh Fri Mar 18 20:03:56 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mrisp_paint -a 5 /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/rh.average.curvature.filled.buckner40.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv averaging curvature patterns 5 times... reading surface from ../surf/rh.sphere.reg... reading template parameterization from /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/rh.average.curvature.filled.buckner40.tif... writing curvature file to ../surf/rh.avg_curv... #----------------------------------------- #@# Cortical Parc rh Fri Mar 18 20:03:57 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 Freesurfer rh ../surf/rh.sphere.reg /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ../label/rh.aparc.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs... reading color table from GCSA file.... average std = 0.7 using min determinant for regularization = 0.006 0 singular and 311 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 808 labels changed using aseg relabeling using gibbs priors... 000: 2250 changed, 97884 examined... 001: 535 changed, 9777 examined... 002: 143 changed, 3003 examined... 003: 51 changed, 847 examined... 004: 28 changed, 311 examined... 005: 11 changed, 176 examined... 006: 9 changed, 73 examined... 007: 4 changed, 49 examined... 008: 3 changed, 24 examined... 009: 2 changed, 17 examined... 010: 0 changed, 10 examined... 199 labels changed using aseg 000: 90 total segments, 52 labels (309 vertices) changed 001: 39 total segments, 1 labels (1 vertices) changed 002: 38 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 41 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 916 vertices marked for relabeling... 916 labels changed in reclassification. writing output to ../label/rh.aparc.annot... classification took 0 minutes and 37 seconds. #-------------------------------------------- #@# Make Pial Surf rh Fri Mar 18 20:04:34 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_make_surfaces -white NOWRITE -mgz -T1 brain.finalsurfs Freesurfer rh -white NOWRITE indicates that white, curv, area, and cortex.label files will not be written... INFO: assuming MGZ format for volumes. using brain.finalsurfs as T1 volume... $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading volume /tmp/surfaKCaG0free/MRI/Freesurfer/mri/filled.mgz... reading volume /tmp/surfaKCaG0free/MRI/Freesurfer/mri/brain.finalsurfs.mgz... reading volume /tmp/surfaKCaG0free/MRI/Freesurfer/mri/wm.mgz... 10109 bright wm thresholded. 4486 bright non-wm voxels segmented. reading original surface position from /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.orig... computing class statistics... border white: 173912 voxels (1.04%) border gray 218602 voxels (1.30%) WM (94.0): 95.6 +- 8.0 [70.0 --> 110.0] GM (84.0) : 82.6 +- 10.3 [30.0 --> 110.0] setting MIN_GRAY_AT_WHITE_BORDER to 65.7 (was 70) setting MAX_BORDER_WHITE to 112.0 (was 105) setting MIN_BORDER_WHITE to 76.0 (was 85) setting MAX_CSF to 55.4 (was 40) setting MAX_GRAY to 96.0 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 70.9 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 45.1 (was 40) smoothing contralateral hemisphere... using class modes intead of means, discounting robust sigmas.... intensity peaks found at WM=104, GM=76 mean inside = 95.2, mean outside = 80.9 smoothing surface for 5 iterations... reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) repositioning cortical surface to gray/white boundary reading volume /tmp/surfaKCaG0free/MRI/Freesurfer/mri/aseg.mgz... smoothing T1 volume with sigma = 2.000 vertex spacing 0.81 +- 0.25 (0.01-->7.54) (max @ vno 79283 --> 87452) face area 0.28 +- 0.15 (0.00-->6.90) mean absolute distance = 0.73 +- 0.95 3208 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... inhibiting deformation at non-cortical midline structures... deleting segment 0 with 7 points - only 0.00% unknown deleting segment 1 with 121 points - only 13.22% unknown deleting segment 2 with 19 points - only 0.00% unknown deleting segment 3 with 5 points - only 0.00% unknown deleting segment 4 with 37 points - only 0.00% unknown deleting segment 6 with 10 points - only 0.00% unknown deleting segment 7 with 74 points - only 0.00% unknown deleting segment 8 with 64 points - only 0.00% unknown deleting segment 9 with 14 points - only 0.00% unknown deleting segment 10 with 574 points - only 0.00% unknown deleting segment 11 with 44 points - only 0.00% unknown deleting segment 12 with 173 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 14 with 91 points - only 0.00% unknown deleting segment 15 with 14 points - only 0.00% unknown deleting segment 16 with 30 points - only 0.00% unknown deleting segment 17 with 7 points - only 0.00% unknown deleting segment 18 with 13 points - only 0.00% unknown deleting segment 19 with 24 points - only 0.00% unknown deleting segment 20 with 94 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 21 with 1 points - only 0.00% unknown mean border=85.4, 368 (344) missing vertices, mean dist 0.2 [0.7 (%37.2)->0.7 (%62.8))] %70 local maxima, %24 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=2.0, host=rc-ru, nav=4, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 complete_dist_mat 0 rms 0 smooth_averages 0 remove_neg 0 ico_order 0 which_surface 0 target_radius 0.000000 nfields 0 scale 0.000000 desired_rms_height 0.000000 momentum 0.000000 nbhd_size 0 max_nbrs 0 niterations 25 nsurfaces 0 SURFACES 3 flags 0 (0) use curv 0 no sulc 0 no rigid align 0 mris->nsize 2 mris->hemisphere 1 randomSeed 0 smoothing T1 volume with sigma = 1.000 vertex spacing 0.91 +- 0.29 (0.09-->7.57) (max @ vno 79283 --> 87452) face area 0.28 +- 0.15 (0.00-->7.46) mean absolute distance = 0.39 +- 0.63 2472 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=5982097.0, rms=14.13 001: dt: 0.5000, sse=5878932.0, rms=11.542 (0.000%) 002: dt: 0.5000, sse=5634324.0, rms=9.523 (0.000%) 003: dt: 0.5000, sse=5531255.0, rms=8.144 (0.000%) 004: dt: 0.5000, sse=5444873.5, rms=7.065 (0.000%) 005: dt: 0.5000, sse=5353179.5, rms=6.228 (0.000%) 006: dt: 0.5000, sse=5343832.0, rms=5.717 (0.000%) 007: dt: 0.5000, sse=5346269.0, rms=5.412 (0.000%) 008: dt: 0.5000, sse=5364868.5, rms=5.244 (0.000%) 009: dt: 0.5000, sse=5330524.5, rms=5.154 (0.000%) 010: dt: 0.5000, sse=5379005.0, rms=5.059 (0.000%) rms = 5.04, time step reduction 1 of 3 to 0.250... 011: dt: 0.5000, sse=5331227.5, rms=5.035 (0.000%) 012: dt: 0.2500, sse=3647505.2, rms=4.554 (0.000%) 013: dt: 0.2500, sse=3496949.5, rms=4.458 (0.000%) rms = 4.45, time step reduction 2 of 3 to 0.125... 014: dt: 0.2500, sse=3416316.8, rms=4.449 (0.000%) 015: dt: 0.1250, sse=3341211.2, rms=4.344 (0.000%) rms = 4.31, time step reduction 3 of 3 to 0.062... 016: dt: 0.1250, sse=3317937.0, rms=4.309 (0.000%) positioning took 1.2 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 168 points - only 22.02% unknown deleting segment 1 with 71 points - only 0.00% unknown deleting segment 2 with 15 points - only 0.00% unknown deleting segment 3 with 67 points - only 0.00% unknown deleting segment 4 with 23 points - only 0.00% unknown removing 3 vertex label from ripped group deleting segment 5 with 3 points - only 0.00% unknown deleting segment 6 with 259 points - only 0.00% unknown deleting segment 7 with 180 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 11 with 9 points - only 0.00% unknown deleting segment 12 with 463 points - only 0.00% unknown deleting segment 13 with 169 points - only 0.00% unknown deleting segment 14 with 43 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 16 with 122 points - only 0.00% unknown deleting segment 17 with 11 points - only 0.00% unknown deleting segment 18 with 5 points - only 0.00% unknown deleting segment 19 with 54 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 20 with 2 points - only 0.00% unknown deleting segment 21 with 189 points - only 0.00% unknown deleting segment 22 with 22 points - only 0.00% unknown mean border=88.1, 369 (91) missing vertices, mean dist -0.2 [0.4 (%75.8)->0.3 (%24.2))] %81 local maxima, %14 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=1.0, host=rc-ru, nav=2, nbrs=2, l_repulse=5.000, l_tspring=1.000, l_nspring=0.500, l_intensity=0.200, l_curv=1.000 mom=0.00, dt=0.50 smoothing T1 volume with sigma = 0.500 vertex spacing 0.90 +- 0.29 (0.07-->7.52) (max @ vno 79283 --> 87452) face area 0.34 +- 0.19 (0.00-->9.94) mean absolute distance = 0.29 +- 0.45 2362 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3606905.2, rms=5.40 017: dt: 0.5000, sse=4039913.5, rms=4.573 (0.000%) 018: dt: 0.5000, sse=4178836.8, rms=4.351 (0.000%) rms = 4.36, time step reduction 1 of 3 to 0.250... 019: dt: 0.2500, sse=3796412.2, rms=4.040 (0.000%) 020: dt: 0.2500, sse=3684630.5, rms=3.943 (0.000%) rms = 3.92, time step reduction 2 of 3 to 0.125... 021: dt: 0.2500, sse=3637783.0, rms=3.917 (0.000%) 022: dt: 0.1250, sse=3566074.0, rms=3.797 (0.000%) rms = 3.78, time step reduction 3 of 3 to 0.062... 023: dt: 0.1250, sse=3548799.5, rms=3.780 (0.000%) positioning took 0.6 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 99 points - only 0.00% unknown deleting segment 1 with 175 points - only 22.29% unknown deleting segment 2 with 18 points - only 0.00% unknown deleting segment 3 with 71 points - only 0.00% unknown deleting segment 4 with 6 points - only 0.00% unknown deleting segment 5 with 27 points - only 0.00% unknown deleting segment 6 with 271 points - only 0.00% unknown deleting segment 7 with 185 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 9 with 13 points - only 0.00% unknown deleting segment 10 with 543 points - only 0.00% unknown deleting segment 12 with 179 points - only 0.00% unknown deleting segment 13 with 53 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 16 with 112 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 17 with 1 points - only 0.00% unknown deleting segment 18 with 56 points - only 0.00% unknown deleting segment 19 with 206 points - only 0.00% unknown deleting segment 20 with 22 points - only 0.00% unknown mean border=89.8, 439 (74) missing vertices, mean dist -0.1 [0.3 (%67.7)->0.3 (%32.3))] %86 local maxima, % 8 large gradients and % 0 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.5, host=rc-ru, 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 +- 0.29 (0.06-->7.48) (max @ vno 79283 --> 87452) face area 0.33 +- 0.19 (0.00-->9.52) mean absolute distance = 0.25 +- 0.37 2359 vertices more than 2 sigmas from mean. averaging target values for 5 iterations... 000: dt: 0.0000, sse=3606347.5, rms=4.27 rms = 4.24, time step reduction 1 of 3 to 0.250... 024: dt: 0.5000, sse=4052482.0, rms=4.237 (0.000%) 025: dt: 0.2500, sse=3757146.2, rms=3.693 (0.000%) 026: dt: 0.2500, sse=3726148.8, rms=3.641 (0.000%) rms = 3.63, time step reduction 2 of 3 to 0.125... 027: dt: 0.2500, sse=3703520.2, rms=3.635 (0.000%) 028: dt: 0.1250, sse=3614916.5, rms=3.497 (0.000%) rms = 3.45, time step reduction 3 of 3 to 0.062... 029: dt: 0.1250, sse=3605592.0, rms=3.454 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... deleting segment 0 with 102 points - only 0.00% unknown deleting segment 1 with 182 points - only 21.98% unknown deleting segment 2 with 19 points - only 0.00% unknown deleting segment 3 with 76 points - only 0.00% unknown deleting segment 4 with 27 points - only 0.00% unknown deleting segment 5 with 281 points - only 0.00% unknown deleting segment 6 with 196 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 8 with 9 points - only 0.00% unknown deleting segment 9 with 546 points - only 0.00% unknown deleting segment 10 with 182 points - only 0.00% unknown deleting segment 11 with 61 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 13 with 117 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 14 with 1 points - only 0.00% unknown deleting segment 15 with 58 points - only 0.00% unknown removing 1 vertex label from ripped group deleting segment 16 with 1 points - only 0.00% unknown deleting segment 17 with 210 points - only 0.00% unknown deleting segment 18 with 22 points - only 0.00% unknown mean border=90.2, 496 (70) missing vertices, mean dist -0.0 [0.3 (%54.5)->0.2 (%45.5))] %87 local maxima, % 6 large gradients and % 1 min vals, 0 gradients ignored tol=1.0e-04, sigma=0.2, host=rc-ru, 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=3620174.0, rms=3.60 rms = 4.06, time step reduction 1 of 3 to 0.250... 030: dt: 0.2500, sse=3713624.5, rms=3.329 (0.000%) rms = 3.43, time step reduction 2 of 3 to 0.125... 031: dt: 0.1250, sse=3721938.8, rms=3.278 (0.000%) 032: dt: 0.1250, sse=3811271.2, rms=3.177 (0.000%) rms = 3.14, time step reduction 3 of 3 to 0.062... 033: dt: 0.1250, sse=3889719.0, rms=3.136 (0.000%) positioning took 0.4 minutes inhibiting deformation at non-cortical midline structures... removing 3 vertex label from ripped group removing 1 vertex label from ripped group deleting segment 3 with 1 points - only 0.00% unknown removing 2 vertex label from ripped group deleting segment 4 with 2 points - only 0.00% unknown smoothing surface for 5 iterations... mean border=66.5, 465 (465) missing vertices, mean dist 1.8 [1.2 (%0.6)->3.1 (%99.4))] %17 local maxima, %37 large gradients and %41 min vals, 2479 gradients ignored tol=1.0e-04, sigma=2.0, host=rc-ru, 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=12987313.0, rms=24.23 001: dt: 0.5000, sse=10346039.0, rms=20.984 (0.000%) 002: dt: 0.5000, sse=8395848.0, rms=18.244 (0.000%) 003: dt: 0.5000, sse=7042400.5, rms=16.027 (0.000%) 004: dt: 0.5000, sse=6239692.0, rms=14.326 (0.000%) 005: dt: 0.5000, sse=5737284.0, rms=13.003 (0.000%) 006: dt: 0.5000, sse=5421180.5, rms=11.996 (0.000%) 007: dt: 0.5000, sse=5194361.0, rms=11.209 (0.000%) 008: dt: 0.5000, sse=5083360.5, rms=10.582 (0.000%) 009: dt: 0.5000, sse=5039497.5, rms=10.035 (0.000%) 010: dt: 0.5000, sse=5030446.5, rms=9.574 (0.000%) 011: dt: 0.5000, sse=5059454.5, rms=9.087 (0.000%) 012: dt: 0.5000, sse=5118978.0, rms=8.656 (0.000%) 013: dt: 0.5000, sse=5112983.0, rms=8.180 (0.000%) 014: dt: 0.5000, sse=5180723.5, rms=7.752 (0.000%) 015: dt: 0.5000, sse=5192625.0, rms=7.361 (0.000%) 016: dt: 0.5000, sse=5265965.0, rms=6.971 (0.000%) 017: dt: 0.5000, sse=5306932.0, rms=6.632 (0.000%) 018: dt: 0.5000, sse=5401500.5, rms=6.349 (0.000%) 019: dt: 0.5000, sse=5432001.0, rms=6.116 (0.000%) 020: dt: 0.5000, sse=5466364.0, rms=5.891 (0.000%) 021: dt: 0.5000, sse=5496279.5, rms=5.719 (0.000%) 022: dt: 0.5000, sse=5565482.5, rms=5.570 (0.000%) 023: dt: 0.5000, sse=5559262.5, rms=5.477 (0.000%) 024: dt: 0.5000, sse=5598314.5, rms=5.397 (0.000%) 025: dt: 0.5000, sse=5585376.5, rms=5.339 (0.000%) 026: dt: 0.5000, sse=5618820.0, rms=5.277 (0.000%) rms = 5.26, time step reduction 1 of 3 to 0.250... 027: dt: 0.5000, sse=5604078.5, rms=5.262 (0.000%) 028: dt: 0.2500, sse=4556385.0, rms=4.738 (0.000%) 029: dt: 0.2500, sse=4468917.5, rms=4.612 (0.000%) rms = 4.64, time step reduction 2 of 3 to 0.125... 030: dt: 0.1250, sse=4373360.5, rms=4.497 (0.000%) positioning took 2.3 minutes mean border=64.6, 3189 (263) missing vertices, mean dist 0.2 [0.3 (%38.2)->0.7 (%61.8))] %34 local maxima, %26 large gradients and %32 min vals, 1303 gradients ignored tol=1.0e-04, sigma=1.0, host=rc-ru, 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=4983419.5, rms=6.15 031: dt: 0.5000, sse=5318907.5, rms=5.950 (0.000%) 032: dt: 0.5000, sse=5922041.5, rms=5.407 (0.000%) rms = 5.66, time step reduction 1 of 3 to 0.250... 033: dt: 0.2500, sse=5250147.0, rms=4.888 (0.000%) 034: dt: 0.2500, sse=5010841.0, rms=4.808 (0.000%) rms = 4.92, time step reduction 2 of 3 to 0.125... 035: dt: 0.1250, sse=4921573.0, rms=4.684 (0.000%) 036: dt: 0.1250, sse=4799841.5, rms=4.534 (0.000%) 037: dt: 0.1250, sse=4766589.0, rms=4.471 (0.000%) rms = 4.45, time step reduction 3 of 3 to 0.062... 038: dt: 0.1250, sse=4766445.5, rms=4.447 (0.000%) positioning took 0.7 minutes mean border=63.6, 3278 (245) missing vertices, mean dist 0.2 [0.2 (%35.8)->0.5 (%64.2))] %44 local maxima, %16 large gradients and %32 min vals, 1446 gradients ignored tol=1.0e-04, sigma=0.5, host=rc-ru, 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=4832402.5, rms=4.71 rms = 5.41, time step reduction 1 of 3 to 0.250... 039: dt: 0.2500, sse=4733484.5, rms=4.503 (0.000%) rms = 4.49, time step reduction 2 of 3 to 0.125... 040: dt: 0.2500, sse=4857308.5, rms=4.493 (0.000%) 041: dt: 0.1250, sse=4771544.5, rms=4.321 (0.000%) 042: dt: 0.1250, sse=4815655.0, rms=4.234 (0.000%) rms = 4.20, time step reduction 3 of 3 to 0.062... 043: dt: 0.1250, sse=4859747.0, rms=4.203 (0.000%) positioning took 0.4 minutes mean border=63.2, 5583 (238) missing vertices, mean dist 0.1 [0.2 (%39.3)->0.4 (%60.7))] %46 local maxima, %13 large gradients and %31 min vals, 1338 gradients ignored tol=1.0e-04, sigma=0.2, host=rc-ru, 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 /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.pial... writing smoothed curvature to rh.curv.pial 000: dt: 0.0000, sse=4879885.0, rms=4.31 rms = 4.98, time step reduction 1 of 3 to 0.250... 044: dt: 0.2500, sse=4874359.0, rms=4.162 (0.000%) rms = 4.16, time step reduction 2 of 3 to 0.125... 045: dt: 0.2500, sse=5164771.5, rms=4.155 (0.000%) 046: dt: 0.1250, sse=5063286.5, rms=4.008 (0.000%) 047: dt: 0.1250, sse=5122234.0, rms=3.916 (0.000%) rms = 3.88, time step reduction 3 of 3 to 0.062... 048: dt: 0.1250, sse=5169657.5, rms=3.881 (0.000%) positioning took 0.4 minutes writing curvature file /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.curv.pial writing smoothed area to rh.area.pial writing curvature file /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.area.pial vertex spacing 1.09 +- 0.52 (0.04-->8.97) (max @ vno 79283 --> 87452) face area 0.47 +- 0.41 (0.00-->14.91) measuring cortical thickness... writing cortical thickness estimate to 'thickness' file. 0 of 97884 vertices processed 25000 of 97884 vertices processed 50000 of 97884 vertices processed 75000 of 97884 vertices processed 0 of 97884 vertices processed 25000 of 97884 vertices processed 50000 of 97884 vertices processed 75000 of 97884 vertices processed thickness calculation complete, 1985:6935 truncations. 15518 vertices at 0 distance 47603 vertices at 1 distance 54693 vertices at 2 distance 37289 vertices at 3 distance 18608 vertices at 4 distance 7421 vertices at 5 distance 2662 vertices at 6 distance 1041 vertices at 7 distance 489 vertices at 8 distance 271 vertices at 9 distance 191 vertices at 10 distance 161 vertices at 11 distance 133 vertices at 12 distance 122 vertices at 13 distance 96 vertices at 14 distance 108 vertices at 15 distance 83 vertices at 16 distance 56 vertices at 17 distance 42 vertices at 18 distance 25 vertices at 19 distance 68 vertices at 20 distance writing curvature file /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.thickness positioning took 8.7 minutes #-------------------------------------------- #@# Surf Volume rh Fri Mar 18 20:13:19 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/surf mris_calc -o rh.area.mid rh.area add rh.area.pial Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.area.mid rh.area.mid div 2 Saving result to 'rh.area.mid' (type = MRI_CURV_FILE) [ ok ] mris_calc -o rh.volume rh.area.mid mul rh.thickness Saving result to 'rh.volume' (type = MRI_CURV_FILE) [ ok ] #----------------------------------------- #@# WM/GM Contrast rh Fri Mar 18 20:13:19 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts pctsurfcon --s Freesurfer --rh-only Log file is /tmp/surfaKCaG0free/MRI/Freesurfer/scripts/pctsurfcon.log Fri Mar 18 20:13:19 EDT 2016 setenv SUBJECTS_DIR /tmp/surfaKCaG0free/MRI cd /tmp/surfaKCaG0free/MRI/Freesurfer/scripts /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/bin/pctsurfcon $Id: pctsurfcon,v 1.11.2.1 2011/11/10 20:37:10 nicks Exp $ Linux rc-russia 3.14.8-mosix #1 SMP Thu Jun 19 12:56:58 EDT 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 mri_vol2surf --mov /tmp/surfaKCaG0free/MRI/Freesurfer/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --projdist -1 --o /tmp/surfaKCaG0free/MRI/Freesurfer/surf/tmp.pctsurfcon.15447/rh.wm.mgh --regheader Freesurfer --cortex srcvol = /tmp/surfaKCaG0free/MRI/Freesurfer/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjDist = -1 reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /tmp/surfaKCaG0free/MRI/Freesurfer/mri/orig.mgz as target reference. Loading label /tmp/surfaKCaG0free/MRI/Freesurfer/label/rh.cortex.label Reading surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 -1 -1 -1 using old Done mapping volume to surface Number of source voxels hit = 49877 Masking with /tmp/surfaKCaG0free/MRI/Freesurfer/label/rh.cortex.label Writing to /tmp/surfaKCaG0free/MRI/Freesurfer/surf/tmp.pctsurfcon.15447/rh.wm.mgh Dim: 97884 1 1 mri_vol2surf --mov /tmp/surfaKCaG0free/MRI/Freesurfer/mri/rawavg.mgz --hemi rh --noreshape --interp trilinear --o /tmp/surfaKCaG0free/MRI/Freesurfer/surf/tmp.pctsurfcon.15447/rh.gm.mgh --projfrac 0.3 --regheader Freesurfer --cortex srcvol = /tmp/surfaKCaG0free/MRI/Freesurfer/mri/rawavg.mgz srcreg unspecified srcregold = 0 srcwarp unspecified surf = white hemi = rh ProjFrac = 0.3 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Computing registration from header. Using /tmp/surfaKCaG0free/MRI/Freesurfer/mri/orig.mgz as target reference. Loading label /tmp/surfaKCaG0free/MRI/Freesurfer/label/rh.cortex.label Reading surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Done reading source surface Reading thickness /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.3 0.3 0.3 using old Done mapping volume to surface Number of source voxels hit = 63223 Masking with /tmp/surfaKCaG0free/MRI/Freesurfer/label/rh.cortex.label Writing to /tmp/surfaKCaG0free/MRI/Freesurfer/surf/tmp.pctsurfcon.15447/rh.gm.mgh Dim: 97884 1 1 mri_concat /tmp/surfaKCaG0free/MRI/Freesurfer/surf/tmp.pctsurfcon.15447/rh.wm.mgh /tmp/surfaKCaG0free/MRI/Freesurfer/surf/tmp.pctsurfcon.15447/rh.gm.mgh --paired-diff-norm --mul 100 --o /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.w-g.pct.mgh ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing Combining pairs nframes = 1 Multiplying by 100.000000 Writing to /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.w-g.pct.mgh mri_segstats --in /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.w-g.pct.mgh --annot Freesurfer rh aparc --sum /tmp/surfaKCaG0free/MRI/Freesurfer/stats/rh.w-g.pct.stats --snr $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --in /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.w-g.pct.mgh --annot Freesurfer rh aparc --sum /tmp/surfaKCaG0free/MRI/Freesurfer/stats/rh.w-g.pct.stats --snr sysname Linux hostname rc-russia machine x86_64 user rudolphpienaar UseRobust 0 Constructing seg from annotation Reading annotation reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 2000 Loading /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.w-g.pct.mgh Vertex Area is 0.655759 mm^3 Generating list of segmentation ids Found 36 segmentations Computing statistics for each segmentation 0 2000 unknown 0 0.000 1 2001 bankssts 1002 675.747 2 2002 caudalanteriorcingulate 753 459.460 3 2003 caudalmiddlefrontal 2853 1912.906 4 2004 corpuscallosum 0 0.000 5 2005 cuneus 1314 877.637 6 2006 entorhinal 296 187.548 7 2007 fusiform 3039 1936.559 8 2008 inferiorparietal 4506 2942.612 9 2009 inferiortemporal 3593 2396.133 10 2010 isthmuscingulate 900 561.473 11 2011 lateraloccipital 4981 3220.491 12 2012 lateralorbitofrontal 3193 2126.500 13 2013 lingual 2910 1870.408 14 2014 medialorbitofrontal 1688 1176.776 15 2015 middletemporal 3569 2383.953 16 2016 parahippocampal 604 381.820 17 2017 paracentral 1730 1157.076 18 2018 parsopercularis 1206 804.430 19 2019 parsorbitalis 915 590.713 20 2020 parstriangularis 1484 997.429 21 2021 pericalcarine 1764 1274.514 22 2022 postcentral 5864 3761.106 23 2023 posteriorcingulate 1164 781.063 24 2024 precentral 5376 3480.007 25 2025 precuneus 4720 3083.198 26 2026 rostralanteriorcingulate 582 386.525 27 2027 rostralmiddlefrontal 6317 4174.739 28 2028 superiorfrontal 7453 4919.376 29 2029 superiorparietal 6886 4415.670 30 2030 superiortemporal 3852 2437.093 31 2031 supramarginal 3585 2506.652 32 2032 frontalpole 355 228.279 33 2033 temporalpole 580 359.724 34 2034 transversetemporal 421 252.328 35 2035 insula 2083 1371.792 Reporting on 34 segmentations mri_segstats done Cleaning up #----------------------------------------- #@# Parcellation Stats rh Fri Mar 18 20:13:24 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab Freesurfer rh white computing statistics for each annotation in ../label/rh.aparc.annot. reading volume /tmp/surfaKCaG0free/MRI/Freesurfer/mri/wm.mgz... reading input surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white... reading input pial surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.pial... reading input white surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1002 676 2268 3.043 0.587 0.154 0.146 47 4.4 bankssts 753 459 1893 3.683 1.054 0.143 0.063 13 2.4 caudalanteriorcingulate 2853 1913 7063 2.646 1.129 0.174 0.102 97 11.5 caudalmiddlefrontal 1314 878 2913 2.637 0.752 0.209 0.233 85 13.2 cuneus 296 188 1169 3.817 0.463 0.122 0.054 3 0.6 entorhinal 3039 1937 7223 3.172 0.730 0.147 0.079 94 11.2 fusiform 4506 2943 9376 2.628 0.930 0.158 0.104 185 16.5 inferiorparietal 3593 2396 11758 3.547 0.755 0.160 0.077 72 11.1 inferiortemporal 900 561 1404 2.332 0.784 0.159 0.069 21 2.2 isthmuscingulate 4981 3220 8592 2.296 0.724 0.162 0.103 126 25.6 lateraloccipital 3193 2126 8209 3.313 0.940 0.145 0.089 78 12.6 lateralorbitofrontal 2910 1870 5207 2.361 0.610 0.150 0.106 247 14.8 lingual 1688 1177 5118 3.523 0.964 0.160 0.100 78 5.6 medialorbitofrontal 3569 2384 10787 3.357 0.734 0.132 0.055 57 8.0 middletemporal 604 382 1564 3.362 0.770 0.108 0.046 7 1.3 parahippocampal 1730 1157 4131 2.756 0.833 0.140 0.061 53 3.9 paracentral 1206 804 2895 2.954 0.611 0.136 0.050 20 2.6 parsopercularis 915 591 3498 3.731 0.751 0.167 0.086 25 3.1 parsorbitalis 1484 997 3934 3.015 0.780 0.134 0.052 23 3.4 parstriangularis 1764 1275 2422 1.913 0.563 0.144 0.062 29 3.8 pericalcarine 5864 3761 10086 2.231 0.749 0.152 0.087 186 19.1 postcentral 1164 781 1598 2.046 1.037 0.227 0.189 102 6.8 posteriorcingulate 5376 3480 11016 2.577 0.796 0.143 0.068 101 15.8 precentral 4720 3083 10350 2.640 1.111 0.181 0.232 237 27.2 precuneus 582 387 2164 3.889 0.592 0.156 0.081 12 1.6 rostralanteriorcingulate 6317 4175 16725 3.026 0.980 0.165 0.095 180 24.7 rostralmiddlefrontal 7453 4919 21480 3.127 1.080 0.159 0.092 204 29.0 superiorfrontal 6886 4416 13760 2.378 0.811 0.166 0.146 610 32.4 superiorparietal 3852 2437 10393 3.545 0.711 0.129 0.120 147 11.3 superiortemporal 3585 2507 8713 2.734 1.042 0.218 0.368 650 50.8 supramarginal 355 228 1524 4.044 0.517 0.273 3.287 1032 2.9 frontalpole 580 360 2455 4.163 0.527 0.153 0.072 11 1.7 temporalpole 421 252 891 3.009 0.490 0.132 0.049 6 0.8 transversetemporal 2083 1372 5103 3.558 0.845 0.098 0.047 21 2.3 insula #----------------------------------------- #@# Cortical Parc 2 rh Fri Mar 18 20:13:32 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 Freesurfer rh ../surf/rh.sphere.reg /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/rh.destrieux.simple.2009-07-29.gcs ../label/rh.aparc.a2009s.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/rh.destrieux.simple.2009-07-29.gcs... reading color table from GCSA file.... average std = 1.9 0.2 using min determinant for regularization = 0.000 0 singular and 851 ill-conditioned covariance matrices regularized input 1: CURVATURE FILE, flags 0, avgs 0, name sulc input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 17 labels changed using aseg relabeling using gibbs priors... 000: 6931 changed, 97884 examined... 001: 1586 changed, 26980 examined... 002: 455 changed, 8435 examined... 003: 197 changed, 2594 examined... 004: 111 changed, 1136 examined... 005: 56 changed, 620 examined... 006: 38 changed, 333 examined... 007: 24 changed, 241 examined... 008: 16 changed, 137 examined... 009: 3 changed, 78 examined... 010: 2 changed, 23 examined... 011: 1 changed, 13 examined... 012: 0 changed, 7 examined... 4 labels changed using aseg 000: 226 total segments, 147 labels (1489 vertices) changed 001: 87 total segments, 9 labels (29 vertices) changed 002: 78 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 109 changed) rationalizing unknown annotations with cortex label relabeling Medial_wall label... 568 vertices marked for relabeling... 568 labels changed in reclassification. writing output to ../label/rh.aparc.a2009s.annot... classification took 0 minutes and 42 seconds. #----------------------------------------- #@# Parcellation Stats 2 rh Fri Mar 18 20:14:15 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab Freesurfer rh white computing statistics for each annotation in ../label/rh.aparc.a2009s.annot. reading volume /tmp/surfaKCaG0free/MRI/Freesurfer/mri/wm.mgz... reading input surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white... reading input pial surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.pial... reading input white surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Saving annotation colortable ../label/aparc.annot.a2009s.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 578 395 2037 3.784 0.880 0.226 2.040 1035 3.0 G_and_S_frontomargin 714 472 1200 2.232 0.567 0.134 0.054 8 1.7 G_and_S_occipital_inf 1201 777 2715 2.511 0.727 0.153 0.078 56 3.3 G_and_S_paracentral 1048 658 2202 2.757 0.512 0.156 0.085 33 4.1 G_and_S_subcentral 792 529 2831 3.483 0.630 0.216 0.136 30 4.4 G_and_S_transv_frontopol 1861 1243 5256 3.717 0.800 0.126 0.054 24 3.4 G_and_S_cingul-Ant 965 642 1930 2.732 1.189 0.190 0.155 40 6.2 G_and_S_cingul-Mid-Ant 958 641 1814 2.466 1.128 0.194 0.156 58 4.2 G_and_S_cingul-Mid-Post 294 188 496 2.276 0.945 0.231 0.146 11 1.1 G_cingul-Post-dorsal 134 79 295 2.818 0.842 0.189 0.116 6 0.6 G_cingul-Post-ventral 1303 857 2827 2.566 0.760 0.199 0.151 48 6.0 G_cuneus 892 580 2883 3.301 0.550 0.158 0.065 21 2.4 G_front_inf-Opercular 253 148 1019 4.032 0.642 0.159 0.067 6 0.7 G_front_inf-Orbital 705 450 2243 3.219 0.720 0.155 0.073 16 2.2 G_front_inf-Triangul 3909 2513 12491 3.204 1.061 0.185 0.113 152 18.7 G_front_middle 4849 3216 16770 3.320 1.127 0.170 0.099 150 21.1 G_front_sup 342 197 1105 3.972 0.690 0.091 0.130 7 0.3 G_Ins_lg_and_S_cent_ins 239 141 997 4.284 0.561 0.099 0.035 2 0.4 G_insular_short 1777 1067 3964 2.777 0.772 0.177 0.183 71 19.3 G_occipital_middle 990 583 1360 1.888 0.657 0.191 0.171 49 7.1 G_occipital_sup 1078 645 2772 3.262 0.594 0.157 0.098 61 4.4 G_oc-temp_lat-fusifor 1758 1110 3409 2.356 0.602 0.164 0.129 225 12.3 G_oc-temp_med-Lingual 746 465 2333 3.742 0.651 0.132 0.059 12 1.8 G_oc-temp_med-Parahip 2205 1448 7749 3.636 0.754 0.177 0.129 85 12.2 G_orbital 1574 960 4227 2.885 1.087 0.163 0.091 47 5.6 G_pariet_inf-Angular 2293 1525 6152 2.847 1.077 0.229 0.310 395 25.1 G_pariet_inf-Supramar 3181 2100 7977 2.714 0.807 0.172 0.108 449 13.8 G_parietal_sup 2406 1494 4617 2.290 0.741 0.164 0.099 104 9.4 G_postcentral 2071 1260 5023 2.732 0.864 0.150 0.094 54 8.3 G_precentral 2706 1790 7311 2.743 1.039 0.196 0.134 114 14.2 G_precuneus 487 369 1634 2.916 0.732 0.233 0.211 61 3.1 G_rectus 273 182 480 2.450 1.015 0.072 0.027 1 0.1 G_subcallosal 310 186 720 3.154 0.528 0.134 0.043 5 0.5 G_temp_sup-G_T_transv 1427 810 4621 3.807 0.694 0.165 0.269 128 7.8 G_temp_sup-Lateral 551 365 1463 3.504 0.667 0.087 0.024 3 0.5 G_temp_sup-Plan_polar 496 336 1467 3.595 0.761 0.128 0.063 6 1.1 G_temp_sup-Plan_tempo 2468 1601 9206 3.747 0.714 0.179 0.096 64 9.7 G_temporal_inf 2103 1369 7737 3.585 0.680 0.145 0.070 45 6.2 G_temporal_middle 323 232 560 2.483 0.560 0.092 0.018 1 0.2 Lat_Fis-ant-Horizont 63 44 197 3.325 0.441 0.173 0.072 1 0.2 Lat_Fis-ant-Vertical 1169 831 2055 2.802 0.567 0.103 0.025 6 1.3 Lat_Fis-post 2835 1880 4298 2.016 0.670 0.167 0.087 70 8.5 Pole_occipital 1325 841 5654 4.026 0.721 0.163 0.106 35 6.9 Pole_temporal 1621 1127 2384 2.121 0.713 0.123 0.039 13 2.4 S_calcarine 2070 1459 2497 1.878 0.628 0.140 0.075 32 4.7 S_central 1348 884 2283 2.351 0.789 0.161 0.101 36 5.4 S_cingul-Marginalis 293 211 724 3.377 0.710 0.104 0.033 2 0.4 S_circular_insula_ant 823 529 1449 3.369 0.790 0.086 0.023 4 0.7 S_circular_insula_inf 990 689 1900 3.135 0.559 0.101 0.026 5 1.1 S_circular_insula_sup 638 448 1282 3.065 0.601 0.117 0.032 4 0.9 S_collat_transv_ant 334 211 638 2.577 0.711 0.138 0.047 6 0.7 S_collat_transv_post 1360 950 2221 2.311 0.689 0.130 0.054 26 2.6 S_front_inf 1502 1003 2736 2.609 0.636 0.131 0.049 17 2.8 S_front_middle 1974 1281 4388 2.621 0.926 0.152 0.090 47 7.5 S_front_sup 128 88 208 2.451 0.836 0.208 0.110 7 0.4 S_interm_prim-Jensen 1903 1269 2579 1.880 0.658 0.194 0.348 223 16.6 S_intrapariet_and_P_trans 496 381 654 2.027 0.511 0.170 0.140 17 2.6 S_oc_middle_and_Lunatus 707 470 907 1.922 0.533 0.134 0.078 10 2.6 S_oc_sup_and_transversal 573 371 1499 2.954 0.691 0.132 0.063 10 1.5 S_occipital_ant 766 522 1575 3.040 0.613 0.142 0.050 10 1.5 S_oc-temp_lat 1320 899 2226 2.678 0.712 0.106 0.027 10 1.5 S_oc-temp_med_and_Lingual 369 246 817 3.125 0.583 0.143 0.046 4 0.6 S_orbital_lateral 458 325 903 2.542 0.816 0.120 0.032 4 0.6 S_orbital_med-olfact 1277 837 2948 3.614 0.927 0.134 0.058 18 3.3 S_orbital-H_Shaped 1184 776 2302 3.135 0.980 0.139 0.147 54 9.3 S_parieto_occipital 1148 695 1819 3.023 1.051 0.122 0.040 38 2.0 S_pericallosal 1960 1325 2850 2.079 0.632 0.170 0.269 225 20.2 S_postcentral 1089 718 1572 2.173 0.850 0.165 0.097 36 4.7 S_precentral-inf-part 1316 906 2253 2.356 0.656 0.121 0.037 12 2.2 S_precentral-sup-part 219 140 728 4.307 0.701 0.123 0.041 2 0.5 S_suborbital 881 596 1120 1.662 0.903 0.224 0.762 114 11.9 S_subparietal 817 553 1298 2.711 0.444 0.135 0.039 9 1.1 S_temporal_inf 4110 2828 8315 3.035 0.585 0.121 0.058 69 8.3 S_temporal_sup 212 137 512 3.226 0.557 0.100 0.019 2 0.2 S_temporal_transverse #----------------------------------------- #@# Cortical Parc 3 rh Fri Mar 18 20:14:24 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.mgz -seed 1234 Freesurfer rh ../surf/rh.sphere.reg /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/rh.DKTatlas40.gcs ../label/rh.aparc.DKTatlas40.annot setting seed for random number generator to 1234 using ../mri/aseg.mgz aseg volume to correct midline $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading atlas from /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/rh.DKTatlas40.gcs... reading color table from GCSA file.... average std = 0.9 using min determinant for regularization = 0.008 0 singular and 237 ill-conditioned covariance matrices regularized input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature labeling surface... 941 labels changed using aseg relabeling using gibbs priors... 000: 1939 changed, 97884 examined... 001: 480 changed, 8627 examined... 002: 138 changed, 2655 examined... 003: 48 changed, 769 examined... 004: 20 changed, 292 examined... 005: 12 changed, 121 examined... 006: 10 changed, 70 examined... 007: 5 changed, 52 examined... 008: 3 changed, 27 examined... 009: 1 changed, 17 examined... 010: 1 changed, 7 examined... 011: 1 changed, 7 examined... 012: 1 changed, 7 examined... 013: 1 changed, 7 examined... 014: 0 changed, 7 examined... 151 labels changed using aseg 000: 60 total segments, 27 labels (162 vertices) changed 001: 33 total segments, 0 labels (0 vertices) changed 10 filter iterations complete (10 requested, 24 changed) rationalizing unknown annotations with cortex label relabeling unknown label... relabeling corpuscallosum label... 501 vertices marked for relabeling... 501 labels changed in reclassification. writing output to ../label/rh.aparc.DKTatlas40.annot... classification took 0 minutes and 37 seconds. #----------------------------------------- #@# Parcellation Stats 3 rh Fri Mar 18 20:15:01 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/scripts mris_anatomical_stats -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas40.stats -b -a ../label/rh.aparc.DKTatlas40.annot -c ../label/aparc.annot.DKTatlas40.ctab Freesurfer rh white computing statistics for each annotation in ../label/rh.aparc.DKTatlas40.annot. reading volume /tmp/surfaKCaG0free/MRI/Freesurfer/mri/wm.mgz... reading input surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white... reading input pial surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.pial... reading input white surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white... INFO: assuming MGZ format for volumes. INFO: using ../label/rh.cortex.label as mask to calc cortex NumVert, SurfArea and MeanThickness. reading colortable from annotation file... colortable with 36 entries read (originally /Applications/freesurfer/average/colortable_desikan_killiany.txt) Saving annotation colortable ../label/aparc.annot.DKTatlas40.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 749 456 1885 3.691 1.050 0.142 0.061 12 2.4 caudalanteriorcingulate 2933 1959 7170 2.648 1.109 0.171 0.098 96 11.4 caudalmiddlefrontal 1586 1043 3331 2.607 0.760 0.195 0.202 88 13.8 cuneus 278 173 1160 3.845 0.472 0.121 0.057 3 0.5 entorhinal 2680 1718 5821 3.084 0.664 0.141 0.062 77 7.0 fusiform 4277 2759 8620 2.562 0.951 0.161 0.112 186 16.3 inferiorparietal 4039 2674 13556 3.584 0.781 0.162 0.088 89 15.6 inferiortemporal 916 575 1414 2.303 0.792 0.158 0.069 21 2.2 isthmuscingulate 5099 3313 8774 2.292 0.720 0.162 0.102 128 25.7 lateraloccipital 3309 2216 9309 3.486 0.911 0.164 0.438 1113 15.1 lateralorbitofrontal 2933 1886 5270 2.361 0.607 0.150 0.105 248 14.8 lingual 1527 1058 4626 3.338 1.090 0.160 0.102 75 5.5 medialorbitofrontal 4257 2854 12209 3.295 0.714 0.134 0.075 97 11.5 middletemporal 601 380 1555 3.364 0.759 0.109 0.047 7 1.3 parahippocampal 1751 1176 4191 2.755 0.837 0.141 0.061 54 3.9 paracentral 1283 851 3129 2.998 0.621 0.134 0.047 20 2.4 parsopercularis 933 598 3159 3.563 0.756 0.147 0.067 20 2.6 parsorbitalis 1453 991 3603 2.897 0.764 0.132 0.050 21 3.0 parstriangularis 1737 1249 2383 1.917 0.563 0.145 0.062 29 3.8 pericalcarine 6373 4078 11040 2.263 0.752 0.152 0.097 217 23.4 postcentral 1366 908 2080 2.151 1.046 0.231 0.192 115 8.5 posteriorcingulate 5168 3357 10805 2.601 0.803 0.145 0.070 101 15.4 precentral 4888 3182 10658 2.620 1.100 0.181 0.228 243 28.2 precuneus 730 488 2465 3.767 0.731 0.141 0.070 13 1.7 rostralanteriorcingulate 4159 2753 10933 3.006 1.040 0.163 0.091 122 15.8 rostralmiddlefrontal 9792 6448 28050 3.128 1.037 0.161 0.093 263 38.4 superiorfrontal 5933 3824 12257 2.411 0.826 0.168 0.146 573 27.9 superiorparietal 5112 3263 14629 3.593 0.721 0.134 0.107 170 14.5 superiortemporal 3399 2387 8047 2.689 1.025 0.218 0.376 640 48.9 supramarginal 406 246 868 2.976 0.475 0.131 0.049 6 0.7 transversetemporal 1871 1232 4685 3.561 0.829 0.094 0.046 16 2.0 insula #-------------------------------------------- #@# Cortical ribbon mask Fri Mar 18 20:15:10 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon Freesurfer SUBJECTS_DIR is /tmp/surfaKCaG0free/MRI loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 15 writing volume /tmp/surfaKCaG0free/MRI/Freesurfer/mri/ribbon.mgz writing ribbon files #-------------------------------------------- #@# ASeg Stats Fri Mar 18 20:24:10 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/ASegStatsLUT.txt --subject Freesurfer $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/ASegStatsLUT.txt --subject Freesurfer sysname Linux hostname rc-russia machine x86_64 user rudolphpienaar UseRobust 0 atlas_icv (eTIV) = 1147857 mm^3 (det: 1.697168 ) Computing euler number orig.nofix lheno = -116, rheno = -116 orig.nofix lhholes = 59, rhholes = 59 Loading mri/aseg.mgz Getting Brain Volume Statistics lhCtxGM: 209614.986 209806.000 diff= -191.0 pctdiff=-0.091 rhCtxGM: 217115.603 216776.000 diff= 339.6 pctdiff= 0.156 lhCtxWM: 120210.940 122362.000 diff=-2151.1 pctdiff=-1.789 rhCtxWM: 123797.667 123263.000 diff= 534.7 pctdiff= 0.432 SubCortGMVol 42272.000 SupraTentVol 721728.196 (721626.000) diff=102.196 pctdiff=0.014 SupraTentVolNotVent 714614.196 (714512.000) diff=102.196 pctdiff=0.014 BrainSegVol 827331.000 (825220.000) diff=2111.000 pctdiff=0.255 BrainSegVolNotVent 817464.000 (815826.196) diff=1637.804 pctdiff=0.200 BrainSegVolNotVent 817464.000 CerebellumVol 102782.000 VentChorVol 7114.000 3rd4th5thCSF 2753.000 CSFVol 664.000, OptChiasmVol 148.000 MaskVol 1166352.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 50 segmentations Computing statistics for each segmentation 3 4 Left-Lateral-Ventricle 2768 2767.955 4 5 Left-Inf-Lat-Vent 374 373.865 5 7 Left-Cerebellum-White-Matter 7659 7659.159 6 8 Left-Cerebellum-Cortex 43691 43690.996 7 10 Left-Thalamus-Proper 5113 5113.461 8 11 Left-Caudate 3126 3126.111 9 12 Left-Putamen 4032 4032.495 10 13 Left-Pallidum 1207 1206.913 11 14 3rd-Ventricle 801 801.124 12 15 4th-Ventricle 1463 1462.755 13 16 Brain-Stem 12209 12209.275 14 17 Left-Hippocampus 3210 3209.990 15 18 Left-Amygdala 1061 1061.345 16 24 CSF 739 738.751 17 26 Left-Accumbens-area 452 452.443 18 28 Left-VentralDC 2272 2271.612 19 30 Left-vessel 14 14.302 20 31 Left-choroid-plexus 981 980.664 23 43 Right-Lateral-Ventricle 2053 2052.787 24 44 Right-Inf-Lat-Vent 313 313.355 25 46 Right-Cerebellum-White-Matter 9188 9187.591 26 47 Right-Cerebellum-Cortex 43248 43247.801 27 49 Right-Thalamus-Proper 4809 4808.562 28 50 Right-Caudate 2691 2690.525 29 51 Right-Putamen 4311 4310.845 30 52 Right-Pallidum 1159 1159.006 31 53 Right-Hippocampus 3218 3217.710 32 54 Right-Amygdala 1328 1328.276 33 58 Right-Accumbens-area 515 514.978 34 60 Right-VentralDC 2368 2367.572 35 62 Right-vessel 25 25.009 36 63 Right-choroid-plexus 1080 1079.614 37 72 5th-Ventricle 0 0.000 38 77 WM-hypointensities 4486 4485.664 39 78 Left-WM-hypointensities 0 0.000 40 79 Right-WM-hypointensities 0 0.000 41 80 non-WM-hypointensities 18 17.576 42 81 Left-non-WM-hypointensities 0 0.000 43 82 Right-non-WM-hypointensities 0 0.000 44 85 Optic-Chiasm 155 154.875 45 251 CC_Posterior 513 512.842 46 252 CC_Mid_Posterior 207 206.878 47 253 CC_Central 314 313.696 48 254 CC_Mid_Anterior 336 336.339 49 255 CC_Anterior 775 774.636 Reporting on 45 segmentations mri_segstats done #----------------------------------------- #@# AParc-to-ASeg Fri Mar 18 20:27:13 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer mri_aparc2aseg --s Freesurfer --volmask SUBJECTS_DIR /tmp/surfaKCaG0free/MRI subject Freesurfer outvol /tmp/surfaKCaG0free/MRI/Freesurfer/mri/aparc+aseg.mgz useribbon 0 baseoffset 0 RipUnknown 0 Reading lh white surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading lh pial surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.pial Loading lh annotations from /tmp/surfaKCaG0free/MRI/Freesurfer/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading rh pial surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.pial Loading rh annotations from /tmp/surfaKCaG0free/MRI/Freesurfer/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /tmp/surfaKCaG0free/MRI/Freesurfer/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /tmp/surfaKCaG0free/MRI/Freesurfer/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 424771 Used brute-force search on 0 voxels Writing output aseg to /tmp/surfaKCaG0free/MRI/Freesurfer/mri/aparc+aseg.mgz /tmp/surfaKCaG0free/MRI/Freesurfer mri_aparc2aseg --s Freesurfer --volmask --a2009s SUBJECTS_DIR /tmp/surfaKCaG0free/MRI subject Freesurfer outvol /tmp/surfaKCaG0free/MRI/Freesurfer/mri/aparc.a2009s+aseg.mgz useribbon 0 baseoffset 10100 RipUnknown 0 Reading lh white surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading lh pial surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.pial Loading lh annotations from /tmp/surfaKCaG0free/MRI/Freesurfer/label/lh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Reading rh white surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading rh pial surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.pial Loading rh annotations from /tmp/surfaKCaG0free/MRI/Freesurfer/label/rh.aparc.a2009s.annot reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /tmp/surfaKCaG0free/MRI/Freesurfer/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /tmp/surfaKCaG0free/MRI/Freesurfer/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 424771 Used brute-force search on 0 voxels Writing output aseg to /tmp/surfaKCaG0free/MRI/Freesurfer/mri/aparc.a2009s+aseg.mgz #----------------------------------------- #@# WMParc Fri Mar 18 20:29:48 EDT 2016 /tmp/surfaKCaG0free/MRI/Freesurfer mri_aparc2aseg --s Freesurfer --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz SUBJECTS_DIR /tmp/surfaKCaG0free/MRI subject Freesurfer outvol mri/wmparc.mgz useribbon 0 baseoffset 0 labeling wm labeling hypo-intensities as wm dmaxctx 5.000000 RipUnknown 1 CtxSeg /tmp/surfaKCaG0free/MRI/Freesurfer/mri/aparc+aseg.mgz Reading lh white surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading lh pial surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.pial Loading lh annotations from /tmp/surfaKCaG0free/MRI/Freesurfer/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Reading rh white surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading rh pial surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.pial Loading rh annotations from /tmp/surfaKCaG0free/MRI/Freesurfer/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Have color table for lh white annotation Have color table for rh white annotation Loading ribbon segmentation from /tmp/surfaKCaG0free/MRI/Freesurfer/mri/ribbon.mgz Loading filled from /tmp/surfaKCaG0free/MRI/Freesurfer/mri/filled.mgz Ripping vertices labeled as unkown Ripped 6483 vertices from left hemi Ripped 6346 vertices from right hemi Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /tmp/surfaKCaG0free/MRI/Freesurfer/mri/aseg.mgz Loading Ctx Seg File /tmp/surfaKCaG0free/MRI/Freesurfer/mri/aparc+aseg.mgz ASeg Vox2RAS: ----------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 669338 Used brute-force search on 0 voxels Fixing Parahip LH WM Found 3 clusters 0 k 1.000000 1 k 1.000000 2 k 849.000000 Fixing Parahip RH WM Found 2 clusters 0 k 741.000000 1 k 2.000000 Writing output aseg to mri/wmparc.mgz /tmp/surfaKCaG0free/MRI/Freesurfer mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject Freesurfer --surf-wm-vol --ctab /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/WMParcStatsLUT.txt --etiv $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject Freesurfer --surf-wm-vol --ctab /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/WMParcStatsLUT.txt --etiv sysname Linux hostname rc-russia machine x86_64 user rudolphpienaar UseRobust 0 atlas_icv (eTIV) = 1147857 mm^3 (det: 1.697168 ) Loading mri/wmparc.mgz Getting Brain Volume Statistics lhCtxGM: 209614.986 209806.000 diff= -191.0 pctdiff=-0.091 rhCtxGM: 217115.603 216776.000 diff= 339.6 pctdiff= 0.156 lhCtxWM: 120210.940 122362.000 diff=-2151.1 pctdiff=-1.789 rhCtxWM: 123797.667 123263.000 diff= 534.7 pctdiff= 0.432 SubCortGMVol 42272.000 SupraTentVol 721728.196 (721626.000) diff=102.196 pctdiff=0.014 SupraTentVolNotVent 714614.196 (714512.000) diff=102.196 pctdiff=0.014 BrainSegVol 827331.000 (825220.000) diff=2111.000 pctdiff=0.255 BrainSegVolNotVent 817464.000 (815826.196) diff=1637.804 pctdiff=0.200 BrainSegVolNotVent 817464.000 CerebellumVol 102782.000 VentChorVol 7114.000 3rd4th5thCSF 2753.000 CSFVol 664.000, OptChiasmVol 148.000 MaskVol 1166352.000 Loading mri/norm.mgz Loading mri/norm.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 390 segmentations Computing statistics for each segmentation 0 3000 wm-lh-unknown 0 0.000 1 3001 wm-lh-bankssts 2157 2156.536 2 3002 wm-lh-caudalanteriorcingulate 1456 1455.891 3 3003 wm-lh-caudalmiddlefrontal 4260 4260.275 4 3004 wm-lh-corpuscallosum 0 0.000 5 3005 wm-lh-cuneus 1108 1108.426 6 3006 wm-lh-entorhinal 431 431.008 7 3007 wm-lh-fusiform 3174 3174.271 8 3008 wm-lh-inferiorparietal 4913 4912.886 9 3009 wm-lh-inferiortemporal 3614 3614.391 10 3010 wm-lh-isthmuscingulate 1754 1753.919 11 3011 wm-lh-lateraloccipital 5431 5430.702 12 3012 wm-lh-lateralorbitofrontal 4344 4344.020 13 3013 wm-lh-lingual 2674 2674.028 14 3014 wm-lh-medialorbitofrontal 2249 2249.406 15 3015 wm-lh-middletemporal 2934 2933.506 16 3016 wm-lh-parahippocampal 926 925.706 17 3017 wm-lh-paracentral 2376 2375.821 18 3018 wm-lh-parsopercularis 1563 1562.596 19 3019 wm-lh-parsorbitalis 687 687.395 20 3020 wm-lh-parstriangularis 1780 1780.193 21 3021 wm-lh-pericalcarine 1959 1959.142 22 3022 wm-lh-postcentral 5154 5153.604 23 3023 wm-lh-posteriorcingulate 2385 2385.272 24 3024 wm-lh-precentral 7048 7048.269 25 3025 wm-lh-precuneus 5765 5765.181 26 3026 wm-lh-rostralanteriorcingulate 1789 1788.655 27 3027 wm-lh-rostralmiddlefrontal 7661 7661.316 28 3028 wm-lh-superiorfrontal 9758 9757.639 29 3029 wm-lh-superiorparietal 7516 7516.350 30 3030 wm-lh-superiortemporal 3581 3581.158 31 3031 wm-lh-supramarginal 3674 3674.027 32 3032 wm-lh-frontalpole 148 148.171 33 3033 wm-lh-temporalpole 437 436.658 34 3034 wm-lh-transversetemporal 481 480.701 35 3035 wm-lh-insula 5593 5592.795 36 3100 wm-lh-Unknown 0 0.000 37 3101 wm-lh-Corpus_callosum 0 0.000 38 3102 wm-lh-G_and_S_Insula_ONLY_AVERAGE 0 0.000 39 3103 wm-lh-G_cingulate-Isthmus 0 0.000 40 3104 wm-lh-G_cingulate-Main_part 0 0.000 41 3105 wm-lh-G_cuneus 0 0.000 42 3106 wm-lh-G_frontal_inf-Opercular_part 0 0.000 43 3107 wm-lh-G_frontal_inf-Orbital_part 0 0.000 44 3108 wm-lh-G_frontal_inf-Triangular_part 0 0.000 45 3109 wm-lh-G_frontal_middle 0 0.000 46 3110 wm-lh-G_frontal_superior 0 0.000 47 3111 wm-lh-G_frontomarginal 0 0.000 48 3112 wm-lh-G_insular_long 0 0.000 49 3113 wm-lh-G_insular_short 0 0.000 50 3114 wm-lh-G_and_S_occipital_inferior 0 0.000 51 3115 wm-lh-G_occipital_middle 0 0.000 52 3116 wm-lh-G_occipital_superior 0 0.000 53 3117 wm-lh-G_occipit-temp_lat-Or_fusiform 0 0.000 54 3118 wm-lh-G_occipit-temp_med-Lingual_part 0 0.000 55 3119 wm-lh-G_occipit-temp_med-Parahippocampal_part 0 0.000 56 3120 wm-lh-G_orbital 0 0.000 57 3121 wm-lh-G_paracentral 0 0.000 58 3122 wm-lh-G_parietal_inferior-Angular_part 0 0.000 59 3123 wm-lh-G_parietal_inferior-Supramarginal_part 0 0.000 60 3124 wm-lh-G_parietal_superior 0 0.000 61 3125 wm-lh-G_postcentral 0 0.000 62 3126 wm-lh-G_precentral 0 0.000 63 3127 wm-lh-G_precuneus 0 0.000 64 3128 wm-lh-G_rectus 0 0.000 65 3129 wm-lh-G_subcallosal 0 0.000 66 3130 wm-lh-G_subcentral 0 0.000 67 3131 wm-lh-G_temporal_inferior 0 0.000 68 3132 wm-lh-G_temporal_middle 0 0.000 69 3133 wm-lh-G_temp_sup-G_temp_transv_and_interm_S 0 0.000 70 3134 wm-lh-G_temp_sup-Lateral_aspect 0 0.000 71 3135 wm-lh-G_temp_sup-Planum_polare 0 0.000 72 3136 wm-lh-G_temp_sup-Planum_tempolare 0 0.000 73 3137 wm-lh-G_and_S_transverse_frontopolar 0 0.000 74 3138 wm-lh-Lat_Fissure-ant_sgt-ramus_horizontal 0 0.000 75 3139 wm-lh-Lat_Fissure-ant_sgt-ramus_vertical 0 0.000 76 3140 wm-lh-Lat_Fissure-post_sgt 0 0.000 77 3141 wm-lh-Medial_wall 0 0.000 78 3142 wm-lh-Pole_occipital 0 0.000 79 3143 wm-lh-Pole_temporal 0 0.000 80 3144 wm-lh-S_calcarine 0 0.000 81 3145 wm-lh-S_central 0 0.000 82 3146 wm-lh-S_central_insula 0 0.000 83 3147 wm-lh-S_cingulate-Main_part_and_Intracingulate 0 0.000 84 3148 wm-lh-S_cingulate-Marginalis_part 0 0.000 85 3149 wm-lh-S_circular_insula_anterior 0 0.000 86 3150 wm-lh-S_circular_insula_inferior 0 0.000 87 3151 wm-lh-S_circular_insula_superior 0 0.000 88 3152 wm-lh-S_collateral_transverse_ant 0 0.000 89 3153 wm-lh-S_collateral_transverse_post 0 0.000 90 3154 wm-lh-S_frontal_inferior 0 0.000 91 3155 wm-lh-S_frontal_middle 0 0.000 92 3156 wm-lh-S_frontal_superior 0 0.000 93 3157 wm-lh-S_frontomarginal 0 0.000 94 3158 wm-lh-S_intermedius_primus-Jensen 0 0.000 95 3159 wm-lh-S_intraparietal-and_Parietal_transverse 0 0.000 96 3160 wm-lh-S_occipital_anterior 0 0.000 97 3161 wm-lh-S_occipital_middle_and_Lunatus 0 0.000 98 3162 wm-lh-S_occipital_superior_and_transversalis 0 0.000 99 3163 wm-lh-S_occipito-temporal_lateral 0 0.000 100 3164 wm-lh-S_occipito-temporal_medial_and_S_Lingual 0 0.000 101 3165 wm-lh-S_orbital-H_shapped 0 0.000 102 3166 wm-lh-S_orbital_lateral 0 0.000 103 3167 wm-lh-S_orbital_medial-Or_olfactory 0 0.000 104 3168 wm-lh-S_paracentral 0 0.000 105 3169 wm-lh-S_parieto_occipital 0 0.000 106 3170 wm-lh-S_pericallosal 0 0.000 107 3171 wm-lh-S_postcentral 0 0.000 108 3172 wm-lh-S_precentral-Inferior-part 0 0.000 109 3173 wm-lh-S_precentral-Superior-part 0 0.000 110 3174 wm-lh-S_subcentral_ant 0 0.000 111 3175 wm-lh-S_subcentral_post 0 0.000 112 3176 wm-lh-S_suborbital 0 0.000 113 3177 wm-lh-S_subparietal 0 0.000 114 3178 wm-lh-S_supracingulate 0 0.000 115 3179 wm-lh-S_temporal_inferior 0 0.000 116 3180 wm-lh-S_temporal_superior 0 0.000 117 3181 wm-lh-S_temporal_transverse 0 0.000 118 4000 wm-rh-unknown 0 0.000 119 4001 wm-rh-bankssts 1491 1490.855 120 4002 wm-rh-caudalanteriorcingulate 1920 1920.473 121 4003 wm-rh-caudalmiddlefrontal 3684 3683.708 122 4004 wm-rh-corpuscallosum 0 0.000 123 4005 wm-rh-cuneus 988 988.277 124 4006 wm-rh-entorhinal 328 328.188 125 4007 wm-rh-fusiform 3756 3756.423 126 4008 wm-rh-inferiorparietal 6453 6452.542 127 4009 wm-rh-inferiortemporal 3739 3738.855 128 4010 wm-rh-isthmuscingulate 1914 1914.080 129 4011 wm-rh-lateraloccipital 4450 4450.038 130 4012 wm-rh-lateralorbitofrontal 4748 4747.822 131 4013 wm-rh-lingual 2332 2332.487 132 4014 wm-rh-medialorbitofrontal 2125 2124.822 133 4015 wm-rh-middletemporal 3545 3545.240 134 4016 wm-rh-parahippocampal 815 814.786 135 4017 wm-rh-paracentral 2216 2215.616 136 4018 wm-rh-parsopercularis 1267 1266.509 137 4019 wm-rh-parsorbitalis 728 728.239 138 4020 wm-rh-parstriangularis 1729 1729.485 139 4021 wm-rh-pericalcarine 2095 2094.880 140 4022 wm-rh-postcentral 6377 6376.596 141 4023 wm-rh-posteriorcingulate 2369 2368.656 142 4024 wm-rh-precentral 6389 6388.627 143 4025 wm-rh-precuneus 6530 6529.930 144 4026 wm-rh-rostralanteriorcingulate 1256 1255.833 145 4027 wm-rh-rostralmiddlefrontal 8435 8434.847 146 4028 wm-rh-superiorfrontal 10260 10259.510 147 4029 wm-rh-superiorparietal 6448 6447.963 148 4030 wm-rh-superiortemporal 3871 3870.844 149 4031 wm-rh-supramarginal 4452 4452.318 150 4032 wm-rh-frontalpole 223 222.718 151 4033 wm-rh-temporalpole 400 399.829 152 4034 wm-rh-transversetemporal 355 355.449 153 4035 wm-rh-insula 5489 5488.688 154 4100 wm-rh-Unknown 0 0.000 155 4101 wm-rh-Corpus_callosum 0 0.000 156 4102 wm-rh-G_and_S_Insula_ONLY_AVERAGE 0 0.000 157 4103 wm-rh-G_cingulate-Isthmus 0 0.000 158 4104 wm-rh-G_cingulate-Main_part 0 0.000 159 4105 wm-rh-G_cuneus 0 0.000 160 4106 wm-rh-G_frontal_inf-Opercular_part 0 0.000 161 4107 wm-rh-G_frontal_inf-Orbital_part 0 0.000 162 4108 wm-rh-G_frontal_inf-Triangular_part 0 0.000 163 4109 wm-rh-G_frontal_middle 0 0.000 164 4110 wm-rh-G_frontal_superior 0 0.000 165 4111 wm-rh-G_frontomarginal 0 0.000 166 4112 wm-rh-G_insular_long 0 0.000 167 4113 wm-rh-G_insular_short 0 0.000 168 4114 wm-rh-G_and_S_occipital_inferior 0 0.000 169 4115 wm-rh-G_occipital_middle 0 0.000 170 4116 wm-rh-G_occipital_superior 0 0.000 171 4117 wm-rh-G_occipit-temp_lat-Or_fusiform 0 0.000 172 4118 wm-rh-G_occipit-temp_med-Lingual_part 0 0.000 173 4119 wm-rh-G_occipit-temp_med-Parahippocampal_part 0 0.000 174 4120 wm-rh-G_orbital 0 0.000 175 4121 wm-rh-G_paracentral 0 0.000 176 4122 wm-rh-G_parietal_inferior-Angular_part 0 0.000 177 4123 wm-rh-G_parietal_inferior-Supramarginal_part 0 0.000 178 4124 wm-rh-G_parietal_superior 0 0.000 179 4125 wm-rh-G_postcentral 0 0.000 180 4126 wm-rh-G_precentral 0 0.000 181 4127 wm-rh-G_precuneus 0 0.000 182 4128 wm-rh-G_rectus 0 0.000 183 4129 wm-rh-G_subcallosal 0 0.000 184 4130 wm-rh-G_subcentral 0 0.000 185 4131 wm-rh-G_temporal_inferior 0 0.000 186 4132 wm-rh-G_temporal_middle 0 0.000 187 4133 wm-rh-G_temp_sup-G_temp_transv_and_interm_S 0 0.000 188 4134 wm-rh-G_temp_sup-Lateral_aspect 0 0.000 189 4135 wm-rh-G_temp_sup-Planum_polare 0 0.000 190 4136 wm-rh-G_temp_sup-Planum_tempolare 0 0.000 191 4137 wm-rh-G_and_S_transverse_frontopolar 0 0.000 192 4138 wm-rh-Lat_Fissure-ant_sgt-ramus_horizontal 0 0.000 193 4139 wm-rh-Lat_Fissure-ant_sgt-ramus_vertical 0 0.000 194 4140 wm-rh-Lat_Fissure-post_sgt 0 0.000 195 4141 wm-rh-Medial_wall 0 0.000 196 4142 wm-rh-Pole_occipital 0 0.000 197 4143 wm-rh-Pole_temporal 0 0.000 198 4144 wm-rh-S_calcarine 0 0.000 199 4145 wm-rh-S_central 0 0.000 200 4146 wm-rh-S_central_insula 0 0.000 201 4147 wm-rh-S_cingulate-Main_part_and_Intracingulate 0 0.000 202 4148 wm-rh-S_cingulate-Marginalis_part 0 0.000 203 4149 wm-rh-S_circular_insula_anterior 0 0.000 204 4150 wm-rh-S_circular_insula_inferior 0 0.000 205 4151 wm-rh-S_circular_insula_superior 0 0.000 206 4152 wm-rh-S_collateral_transverse_ant 0 0.000 207 4153 wm-rh-S_collateral_transverse_post 0 0.000 208 4154 wm-rh-S_frontal_inferior 0 0.000 209 4155 wm-rh-S_frontal_middle 0 0.000 210 4156 wm-rh-S_frontal_superior 0 0.000 211 4157 wm-rh-S_frontomarginal 0 0.000 212 4158 wm-rh-S_intermedius_primus-Jensen 0 0.000 213 4159 wm-rh-S_intraparietal-and_Parietal_transverse 0 0.000 214 4160 wm-rh-S_occipital_anterior 0 0.000 215 4161 wm-rh-S_occipital_middle_and_Lunatus 0 0.000 216 4162 wm-rh-S_occipital_superior_and_transversalis 0 0.000 217 4163 wm-rh-S_occipito-temporal_lateral 0 0.000 218 4164 wm-rh-S_occipito-temporal_medial_and_S_Lingual 0 0.000 219 4165 wm-rh-S_orbital-H_shapped 0 0.000 220 4166 wm-rh-S_orbital_lateral 0 0.000 221 4167 wm-rh-S_orbital_medial-Or_olfactory 0 0.000 222 4168 wm-rh-S_paracentral 0 0.000 223 4169 wm-rh-S_parieto_occipital 0 0.000 224 4170 wm-rh-S_pericallosal 0 0.000 225 4171 wm-rh-S_postcentral 0 0.000 226 4172 wm-rh-S_precentral-Inferior-part 0 0.000 227 4173 wm-rh-S_precentral-Superior-part 0 0.000 228 4174 wm-rh-S_subcentral_ant 0 0.000 229 4175 wm-rh-S_subcentral_post 0 0.000 230 4176 wm-rh-S_suborbital 0 0.000 231 4177 wm-rh-S_subparietal 0 0.000 232 4178 wm-rh-S_supracingulate 0 0.000 233 4179 wm-rh-S_temporal_inferior 0 0.000 234 4180 wm-rh-S_temporal_superior 0 0.000 235 4181 wm-rh-S_temporal_transverse 0 0.000 236 5001 Left-UnsegmentedWhiteMatter 9710 9709.709 237 5002 Right-UnsegmentedWhiteMatter 10876 10876.057 238 13100 wm_lh_Unknown 0 0.000 239 13101 wm_lh_G_and_S_frontomargin 0 0.000 240 13102 wm_lh_G_and_S_occipital_inf 0 0.000 241 13103 wm_lh_G_and_S_paracentral 0 0.000 242 13104 wm_lh_G_and_S_subcentral 0 0.000 243 13105 wm_lh_G_and_S_transv_frontopol 0 0.000 244 13106 wm_lh_G_and_S_cingul-Ant 0 0.000 245 13107 wm_lh_G_and_S_cingul-Mid-Ant 0 0.000 246 13108 wm_lh_G_and_S_cingul-Mid-Post 0 0.000 247 13109 wm_lh_G_cingul-Post-dorsal 0 0.000 248 13110 wm_lh_G_cingul-Post-ventral 0 0.000 249 13111 wm_lh_G_cuneus 0 0.000 250 13112 wm_lh_G_front_inf-Opercular 0 0.000 251 13113 wm_lh_G_front_inf-Orbital 0 0.000 252 13114 wm_lh_G_front_inf-Triangul 0 0.000 253 13115 wm_lh_G_front_middle 0 0.000 254 13116 wm_lh_G_front_sup 0 0.000 255 13117 wm_lh_G_Ins_lg_and_S_cent_ins 0 0.000 256 13118 wm_lh_G_insular_short 0 0.000 257 13119 wm_lh_G_occipital_middle 0 0.000 258 13120 wm_lh_G_occipital_sup 0 0.000 259 13121 wm_lh_G_oc-temp_lat-fusifor 0 0.000 260 13122 wm_lh_G_oc-temp_med-Lingual 0 0.000 261 13123 wm_lh_G_oc-temp_med-Parahip 0 0.000 262 13124 wm_lh_G_orbital 0 0.000 263 13125 wm_lh_G_pariet_inf-Angular 0 0.000 264 13126 wm_lh_G_pariet_inf-Supramar 0 0.000 265 13127 wm_lh_G_parietal_sup 0 0.000 266 13128 wm_lh_G_postcentral 0 0.000 267 13129 wm_lh_G_precentral 0 0.000 268 13130 wm_lh_G_precuneus 0 0.000 269 13131 wm_lh_G_rectus 0 0.000 270 13132 wm_lh_G_subcallosal 0 0.000 271 13133 wm_lh_G_temp_sup-G_T_transv 0 0.000 272 13134 wm_lh_G_temp_sup-Lateral 0 0.000 273 13135 wm_lh_G_temp_sup-Plan_polar 0 0.000 274 13136 wm_lh_G_temp_sup-Plan_tempo 0 0.000 275 13137 wm_lh_G_temporal_inf 0 0.000 276 13138 wm_lh_G_temporal_middle 0 0.000 277 13139 wm_lh_Lat_Fis-ant-Horizont 0 0.000 278 13140 wm_lh_Lat_Fis-ant-Vertical 0 0.000 279 13141 wm_lh_Lat_Fis-post 0 0.000 280 13142 wm_lh_Medial_wall 0 0.000 281 13143 wm_lh_Pole_occipital 0 0.000 282 13144 wm_lh_Pole_temporal 0 0.000 283 13145 wm_lh_S_calcarine 0 0.000 284 13146 wm_lh_S_central 0 0.000 285 13147 wm_lh_S_cingul-Marginalis 0 0.000 286 13148 wm_lh_S_circular_insula_ant 0 0.000 287 13149 wm_lh_S_circular_insula_inf 0 0.000 288 13150 wm_lh_S_circular_insula_sup 0 0.000 289 13151 wm_lh_S_collat_transv_ant 0 0.000 290 13152 wm_lh_S_collat_transv_post 0 0.000 291 13153 wm_lh_S_front_inf 0 0.000 292 13154 wm_lh_S_front_middle 0 0.000 293 13155 wm_lh_S_front_sup 0 0.000 294 13156 wm_lh_S_interm_prim-Jensen 0 0.000 295 13157 wm_lh_S_intrapariet_and_P_trans 0 0.000 296 13158 wm_lh_S_oc_middle_and_Lunatus 0 0.000 297 13159 wm_lh_S_oc_sup_and_transversal 0 0.000 298 13160 wm_lh_S_occipital_ant 0 0.000 299 13161 wm_lh_S_oc-temp_lat 0 0.000 300 13162 wm_lh_S_oc-temp_med_and_Lingual 0 0.000 301 13163 wm_lh_S_orbital_lateral 0 0.000 302 13164 wm_lh_S_orbital_med-olfact 0 0.000 303 13165 wm_lh_S_orbital-H_Shaped 0 0.000 304 13166 wm_lh_S_parieto_occipital 0 0.000 305 13167 wm_lh_S_pericallosal 0 0.000 306 13168 wm_lh_S_postcentral 0 0.000 307 13169 wm_lh_S_precentral-inf-part 0 0.000 308 13170 wm_lh_S_precentral-sup-part 0 0.000 309 13171 wm_lh_S_suborbital 0 0.000 310 13172 wm_lh_S_subparietal 0 0.000 311 13173 wm_lh_S_temporal_inf 0 0.000 312 13174 wm_lh_S_temporal_sup 0 0.000 313 13175 wm_lh_S_temporal_transverse 0 0.000 314 14100 wm_rh_Unknown 0 0.000 315 14101 wm_rh_G_and_S_frontomargin 0 0.000 316 14102 wm_rh_G_and_S_occipital_inf 0 0.000 317 14103 wm_rh_G_and_S_paracentral 0 0.000 318 14104 wm_rh_G_and_S_subcentral 0 0.000 319 14105 wm_rh_G_and_S_transv_frontopol 0 0.000 320 14106 wm_rh_G_and_S_cingul-Ant 0 0.000 321 14107 wm_rh_G_and_S_cingul-Mid-Ant 0 0.000 322 14108 wm_rh_G_and_S_cingul-Mid-Post 0 0.000 323 14109 wm_rh_G_cingul-Post-dorsal 0 0.000 324 14110 wm_rh_G_cingul-Post-ventral 0 0.000 325 14111 wm_rh_G_cuneus 0 0.000 326 14112 wm_rh_G_front_inf-Opercular 0 0.000 327 14113 wm_rh_G_front_inf-Orbital 0 0.000 328 14114 wm_rh_G_front_inf-Triangul 0 0.000 329 14115 wm_rh_G_front_middle 0 0.000 330 14116 wm_rh_G_front_sup 0 0.000 331 14117 wm_rh_G_Ins_lg_and_S_cent_ins 0 0.000 332 14118 wm_rh_G_insular_short 0 0.000 333 14119 wm_rh_G_occipital_middle 0 0.000 334 14120 wm_rh_G_occipital_sup 0 0.000 335 14121 wm_rh_G_oc-temp_lat-fusifor 0 0.000 336 14122 wm_rh_G_oc-temp_med-Lingual 0 0.000 337 14123 wm_rh_G_oc-temp_med-Parahip 0 0.000 338 14124 wm_rh_G_orbital 0 0.000 339 14125 wm_rh_G_pariet_inf-Angular 0 0.000 340 14126 wm_rh_G_pariet_inf-Supramar 0 0.000 341 14127 wm_rh_G_parietal_sup 0 0.000 342 14128 wm_rh_G_postcentral 0 0.000 343 14129 wm_rh_G_precentral 0 0.000 344 14130 wm_rh_G_precuneus 0 0.000 345 14131 wm_rh_G_rectus 0 0.000 346 14132 wm_rh_G_subcallosal 0 0.000 347 14133 wm_rh_G_temp_sup-G_T_transv 0 0.000 348 14134 wm_rh_G_temp_sup-Lateral 0 0.000 349 14135 wm_rh_G_temp_sup-Plan_polar 0 0.000 350 14136 wm_rh_G_temp_sup-Plan_tempo 0 0.000 351 14137 wm_rh_G_temporal_inf 0 0.000 352 14138 wm_rh_G_temporal_middle 0 0.000 353 14139 wm_rh_Lat_Fis-ant-Horizont 0 0.000 354 14140 wm_rh_Lat_Fis-ant-Vertical 0 0.000 355 14141 wm_rh_Lat_Fis-post 0 0.000 356 14142 wm_rh_Medial_wall 0 0.000 357 14143 wm_rh_Pole_occipital 0 0.000 358 14144 wm_rh_Pole_temporal 0 0.000 359 14145 wm_rh_S_calcarine 0 0.000 360 14146 wm_rh_S_central 0 0.000 361 14147 wm_rh_S_cingul-Marginalis 0 0.000 362 14148 wm_rh_S_circular_insula_ant 0 0.000 363 14149 wm_rh_S_circular_insula_inf 0 0.000 364 14150 wm_rh_S_circular_insula_sup 0 0.000 365 14151 wm_rh_S_collat_transv_ant 0 0.000 366 14152 wm_rh_S_collat_transv_post 0 0.000 367 14153 wm_rh_S_front_inf 0 0.000 368 14154 wm_rh_S_front_middle 0 0.000 369 14155 wm_rh_S_front_sup 0 0.000 370 14156 wm_rh_S_interm_prim-Jensen 0 0.000 371 14157 wm_rh_S_intrapariet_and_P_trans 0 0.000 372 14158 wm_rh_S_oc_middle_and_Lunatus 0 0.000 373 14159 wm_rh_S_oc_sup_and_transversal 0 0.000 374 14160 wm_rh_S_occipital_ant 0 0.000 375 14161 wm_rh_S_oc-temp_lat 0 0.000 376 14162 wm_rh_S_oc-temp_med_and_Lingual 0 0.000 377 14163 wm_rh_S_orbital_lateral 0 0.000 378 14164 wm_rh_S_orbital_med-olfact 0 0.000 379 14165 wm_rh_S_orbital-H_Shaped 0 0.000 380 14166 wm_rh_S_parieto_occipital 0 0.000 381 14167 wm_rh_S_pericallosal 0 0.000 382 14168 wm_rh_S_postcentral 0 0.000 383 14169 wm_rh_S_precentral-inf-part 0 0.000 384 14170 wm_rh_S_precentral-sup-part 0 0.000 385 14171 wm_rh_S_suborbital 0 0.000 386 14172 wm_rh_S_subparietal 0 0.000 387 14173 wm_rh_S_temporal_inf 0 0.000 388 14174 wm_rh_S_temporal_sup 0 0.000 389 14175 wm_rh_S_temporal_transverse 0 0.000 Reporting on 70 segmentations mri_segstats done /tmp/surfaKCaG0free/MRI/Freesurfer/label #-------------------------------------------- #@# BA Labels lh Fri Mar 18 20:38:12 EDT 2016 mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA1.label --trgsubject Freesurfer --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4129 nlabel points Performing mapping from target back to the source label 94903 Number of reverse mapping hits = 367 Checking for and removing duplicates Writing label file ./lh.BA1.label 4496 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA2.label --trgsubject Freesurfer --trglabel ./lh.BA2.label --hemi lh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./lh.BA2.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 7909 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7909 nlabel points Performing mapping from target back to the source label 94903 Number of reverse mapping hits = 574 Checking for and removing duplicates Writing label file ./lh.BA2.label 8483 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA3a.label --trgsubject Freesurfer --trglabel ./lh.BA3a.label --hemi lh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA3a.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./lh.BA3a.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 4077 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4077 nlabel points Performing mapping from target back to the source label 94903 Number of reverse mapping hits = 107 Checking for and removing duplicates Writing label file ./lh.BA3a.label 4184 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA3b.label --trgsubject Freesurfer --trglabel ./lh.BA3b.label --hemi lh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA3b.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./lh.BA3b.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 5983 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5983 nlabel points Performing mapping from target back to the source label 94903 Number of reverse mapping hits = 212 Checking for and removing duplicates Writing label file ./lh.BA3b.label 6195 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA4a.label --trgsubject Freesurfer --trglabel ./lh.BA4a.label --hemi lh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA4a.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./lh.BA4a.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 5784 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5784 nlabel points Performing mapping from target back to the source label 94903 Number of reverse mapping hits = 333 Checking for and removing duplicates Writing label file ./lh.BA4a.label 6117 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA4p.label --trgsubject Freesurfer --trglabel ./lh.BA4p.label --hemi lh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA4p.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./lh.BA4p.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 4070 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4070 nlabel points Performing mapping from target back to the source label 94903 Number of reverse mapping hits = 261 Checking for and removing duplicates Writing label file ./lh.BA4p.label 4331 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA6.label --trgsubject Freesurfer --trglabel ./lh.BA6.label --hemi lh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA6.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./lh.BA6.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 13589 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 13589 nlabel points Performing mapping from target back to the source label 94903 Number of reverse mapping hits = 958 Checking for and removing duplicates Writing label file ./lh.BA6.label 14547 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA44.label --trgsubject Freesurfer --trglabel ./lh.BA44.label --hemi lh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA44.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./lh.BA44.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 4181 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4181 nlabel points Performing mapping from target back to the source label 94903 Number of reverse mapping hits = 184 Checking for and removing duplicates Writing label file ./lh.BA44.label 4365 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA45.label --trgsubject Freesurfer --trglabel ./lh.BA45.label --hemi lh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA45.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./lh.BA45.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 3422 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3422 nlabel points Performing mapping from target back to the source label 94903 Number of reverse mapping hits = 389 Checking for and removing duplicates Writing label file ./lh.BA45.label 3811 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.V1.label --trgsubject Freesurfer --trglabel ./lh.V1.label --hemi lh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.V1.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./lh.V1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 4641 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4641 nlabel points Performing mapping from target back to the source label 94903 Number of reverse mapping hits = 1071 Checking for and removing duplicates Writing label file ./lh.V1.label 5712 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.V2.label --trgsubject Freesurfer --trglabel ./lh.V2.label --hemi lh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.V2.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./lh.V2.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 8114 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8114 nlabel points Performing mapping from target back to the source label 94903 Number of reverse mapping hits = 1740 Checking for and removing duplicates Writing label file ./lh.V2.label 9854 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.MT.label --trgsubject Freesurfer --trglabel ./lh.MT.label --hemi lh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.MT.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./lh.MT.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 2018 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2018 nlabel points Performing mapping from target back to the source label 94903 Number of reverse mapping hits = 109 Checking for and removing duplicates Writing label file ./lh.MT.label 2127 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.perirhinal.label --trgsubject Freesurfer --trglabel ./lh.perirhinal.label --hemi lh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.perirhinal.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./lh.perirhinal.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 1199 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1199 nlabel points Performing mapping from target back to the source label 94903 Number of reverse mapping hits = 31 Checking for and removing duplicates Writing label file ./lh.perirhinal.label 1230 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA1.thresh.label --trgsubject Freesurfer --trglabel ./lh.BA1.thresh.label --hemi lh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA1.thresh.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./lh.BA1.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 1014 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1014 nlabel points Performing mapping from target back to the source label 94903 Number of reverse mapping hits = 110 Checking for and removing duplicates Writing label file ./lh.BA1.thresh.label 1124 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA2.thresh.label --trgsubject Freesurfer --trglabel ./lh.BA2.thresh.label --hemi lh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA2.thresh.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./lh.BA2.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 2092 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2092 nlabel points Performing mapping from target back to the source label 94903 Number of reverse mapping hits = 226 Checking for and removing duplicates Writing label file ./lh.BA2.thresh.label 2318 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA3a.thresh.label --trgsubject Freesurfer --trglabel ./lh.BA3a.thresh.label --hemi lh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA3a.thresh.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./lh.BA3a.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 1504 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1504 nlabel points Performing mapping from target back to the source label 94903 Number of reverse mapping hits = 29 Checking for and removing duplicates Writing label file ./lh.BA3a.thresh.label 1533 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA3b.thresh.label --trgsubject Freesurfer --trglabel ./lh.BA3b.thresh.label --hemi lh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA3b.thresh.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./lh.BA3b.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 1996 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1996 nlabel points Performing mapping from target back to the source label 94903 Number of reverse mapping hits = 65 Checking for and removing duplicates Writing label file ./lh.BA3b.thresh.label 2061 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA4a.thresh.label --trgsubject Freesurfer --trglabel ./lh.BA4a.thresh.label --hemi lh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA4a.thresh.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./lh.BA4a.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 2319 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2319 nlabel points Performing mapping from target back to the source label 94903 Number of reverse mapping hits = 111 Checking for and removing duplicates Writing label file ./lh.BA4a.thresh.label 2430 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA4p.thresh.label --trgsubject Freesurfer --trglabel ./lh.BA4p.thresh.label --hemi lh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA4p.thresh.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./lh.BA4p.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 1549 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1549 nlabel points Performing mapping from target back to the source label 94903 Number of reverse mapping hits = 112 Checking for and removing duplicates Writing label file ./lh.BA4p.thresh.label 1661 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA6.thresh.label --trgsubject Freesurfer --trglabel ./lh.BA6.thresh.label --hemi lh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA6.thresh.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./lh.BA6.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 7035 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 7035 nlabel points Performing mapping from target back to the source label 94903 Number of reverse mapping hits = 383 Checking for and removing duplicates Writing label file ./lh.BA6.thresh.label 7418 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA44.thresh.label --trgsubject Freesurfer --trglabel ./lh.BA44.thresh.label --hemi lh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA44.thresh.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./lh.BA44.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 1912 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1912 nlabel points Performing mapping from target back to the source label 94903 Number of reverse mapping hits = 46 Checking for and removing duplicates Writing label file ./lh.BA44.thresh.label 1958 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA45.thresh.label --trgsubject Freesurfer --trglabel ./lh.BA45.thresh.label --hemi lh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.BA45.thresh.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./lh.BA45.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 1151 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1151 nlabel points Performing mapping from target back to the source label 94903 Number of reverse mapping hits = 88 Checking for and removing duplicates Writing label file ./lh.BA45.thresh.label 1239 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.V1.thresh.label --trgsubject Freesurfer --trglabel ./lh.V1.thresh.label --hemi lh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.V1.thresh.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./lh.V1.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 3405 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3405 nlabel points Performing mapping from target back to the source label 94903 Number of reverse mapping hits = 746 Checking for and removing duplicates Writing label file ./lh.V1.thresh.label 4151 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.V2.thresh.label --trgsubject Freesurfer --trglabel ./lh.V2.thresh.label --hemi lh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.V2.thresh.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./lh.V2.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 3334 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3334 nlabel points Performing mapping from target back to the source label 94903 Number of reverse mapping hits = 878 Checking for and removing duplicates Writing label file ./lh.V2.thresh.label 4212 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.MT.thresh.label --trgsubject Freesurfer --trglabel ./lh.MT.thresh.label --hemi lh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/lh.MT.thresh.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./lh.MT.thresh.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 513 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 513 nlabel points Performing mapping from target back to the source label 94903 Number of reverse mapping hits = 26 Checking for and removing duplicates Writing label file ./lh.MT.thresh.label 539 mri_label2label: Done mris_label2annot --s Freesurfer --hemi lh --ctab /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose Reading ctab /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /tmp/surfaKCaG0free/MRI/Freesurfer/label cmdline mris_label2annot --s Freesurfer --hemi lh --ctab /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/colortable_BA.txt --l lh.BA1.label --l lh.BA2.label --l lh.BA3a.label --l lh.BA3b.label --l lh.BA4a.label --l lh.BA4p.label --l lh.BA6.label --l lh.BA44.label --l lh.BA45.label --l lh.V1.label --l lh.V2.label --l lh.MT.label --l lh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname rc-russia machine x86_64 user rudolphpienaar subject Freesurfer hemi lh SUBJECTS_DIR /tmp/surfaKCaG0free/MRI ColorTable /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT 13 16422433 perirhinal Mapping unhit to unknown Found 62884 unhit vertices Writing annot to /tmp/surfaKCaG0free/MRI/Freesurfer/label/lh.BA.annot mris_label2annot --s Freesurfer --hemi lh --ctab /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose Reading ctab /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /tmp/surfaKCaG0free/MRI/Freesurfer/label cmdline mris_label2annot --s Freesurfer --hemi lh --ctab /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/colortable_BA.txt --l lh.BA1.thresh.label --l lh.BA2.thresh.label --l lh.BA3a.thresh.label --l lh.BA3b.thresh.label --l lh.BA4a.thresh.label --l lh.BA4p.thresh.label --l lh.BA6.thresh.label --l lh.BA44.thresh.label --l lh.BA45.thresh.label --l lh.V1.thresh.label --l lh.V2.thresh.label --l lh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname rc-russia machine x86_64 user rudolphpienaar subject Freesurfer hemi lh SUBJECTS_DIR /tmp/surfaKCaG0free/MRI ColorTable /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT Mapping unhit to unknown Found 76187 unhit vertices Writing annot to /tmp/surfaKCaG0free/MRI/Freesurfer/label/lh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/lh.BA.stats -b -a ./lh.BA.annot -c ./BA.ctab Freesurfer lh white computing statistics for each annotation in ./lh.BA.annot. reading volume /tmp/surfaKCaG0free/MRI/Freesurfer/mri/wm.mgz... reading input surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white... reading input pial surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.pial... reading input white surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/colortable_BA.txt) Saving annotation colortable ./BA.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 1015 595 1849 2.126 0.736 0.210 0.131 76 4.5 BA1 3233 2189 5984 2.272 0.835 0.147 0.086 61 13.2 BA2 809 539 780 1.877 0.517 0.168 0.119 142 5.4 BA3a 1773 1215 2912 1.951 0.756 0.160 0.196 266 12.0 BA3b 1350 898 3313 2.847 0.831 0.187 0.158 102 9.7 BA4a 1059 751 1842 2.257 0.756 0.149 0.057 20 2.3 BA4p 7457 5029 20332 2.963 0.989 0.161 0.102 251 31.9 BA6 1561 1010 3909 2.976 0.764 0.145 0.067 38 3.8 BA44 2367 1539 5754 2.798 0.759 0.138 0.061 38 6.2 BA45 3049 2017 4097 1.868 0.645 0.145 0.072 47 7.8 V1 6370 4063 9966 2.151 0.725 0.171 0.104 165 23.7 V2 1314 878 2660 2.605 0.750 0.145 0.053 18 2.7 MT 662 421 2023 3.717 0.825 0.146 0.063 9 1.7 perirhinal mris_anatomical_stats -mgz -f ../stats/lh.BA.thresh.stats -b -a ./lh.BA.thresh.annot -c ./BA.thresh.ctab Freesurfer lh white computing statistics for each annotation in ./lh.BA.thresh.annot. reading volume /tmp/surfaKCaG0free/MRI/Freesurfer/mri/wm.mgz... reading input surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white... reading input pial surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.pial... reading input white surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/colortable_BA.txt) Saving annotation colortable ./BA.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 659 361 1163 2.140 0.760 0.231 0.183 66 3.4 BA1 1431 950 2506 2.327 0.728 0.134 0.047 21 2.6 BA2 649 432 587 1.860 0.487 0.149 0.053 8 1.4 BA3a 1044 762 1324 1.561 0.466 0.140 0.133 203 2.8 BA3b 1200 819 2906 2.781 0.835 0.169 0.115 53 6.4 BA4a 876 631 1418 2.064 0.706 0.197 0.161 184 8.1 BA4p 4098 2821 11513 3.019 0.936 0.152 0.069 97 10.2 BA6 997 649 2678 3.092 0.722 0.152 0.072 26 2.6 BA44 871 561 2422 2.907 0.700 0.143 0.074 16 3.1 BA45 3173 2105 4358 1.860 0.651 0.147 0.068 51 8.1 V1 3354 2146 5209 2.141 0.727 0.177 0.126 98 13.3 V2 364 246 510 2.190 0.805 0.132 0.034 3 0.5 MT #-------------------------------------------- #@# BA Labels rh Fri Mar 18 20:41:03 EDT 2016 mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA1.label --trgsubject Freesurfer --trglabel ./rh.BA1.label --hemi rh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA1.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./rh.BA1.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 3962 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3962 nlabel points Performing mapping from target back to the source label 97884 Number of reverse mapping hits = 441 Checking for and removing duplicates Writing label file ./rh.BA1.label 4403 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA2.label --trgsubject Freesurfer --trglabel ./rh.BA2.label --hemi rh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA2.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./rh.BA2.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 6687 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6687 nlabel points Performing mapping from target back to the source label 97884 Number of reverse mapping hits = 648 Checking for and removing duplicates Writing label file ./rh.BA2.label 7335 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA3a.label --trgsubject Freesurfer --trglabel ./rh.BA3a.label --hemi rh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA3a.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./rh.BA3a.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 3980 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3980 nlabel points Performing mapping from target back to the source label 97884 Number of reverse mapping hits = 134 Checking for and removing duplicates Writing label file ./rh.BA3a.label 4114 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA3b.label --trgsubject Freesurfer --trglabel ./rh.BA3b.label --hemi rh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA3b.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./rh.BA3b.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 4522 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4522 nlabel points Performing mapping from target back to the source label 97884 Number of reverse mapping hits = 251 Checking for and removing duplicates Writing label file ./rh.BA3b.label 4773 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA4a.label --trgsubject Freesurfer --trglabel ./rh.BA4a.label --hemi rh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA4a.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./rh.BA4a.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 5747 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5747 nlabel points Performing mapping from target back to the source label 97884 Number of reverse mapping hits = 103 Checking for and removing duplicates Writing label file ./rh.BA4a.label 5850 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA4p.label --trgsubject Freesurfer --trglabel ./rh.BA4p.label --hemi rh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA4p.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./rh.BA4p.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 4473 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4473 nlabel points Performing mapping from target back to the source label 97884 Number of reverse mapping hits = 56 Checking for and removing duplicates Writing label file ./rh.BA4p.label 4529 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA6.label --trgsubject Freesurfer --trglabel ./rh.BA6.label --hemi rh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA6.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./rh.BA6.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 12256 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 12256 nlabel points Performing mapping from target back to the source label 97884 Number of reverse mapping hits = 698 Checking for and removing duplicates Writing label file ./rh.BA6.label 12954 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA44.label --trgsubject Freesurfer --trglabel ./rh.BA44.label --hemi rh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA44.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./rh.BA44.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 6912 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6912 nlabel points Performing mapping from target back to the source label 97884 Number of reverse mapping hits = 340 Checking for and removing duplicates Writing label file ./rh.BA44.label 7252 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA45.label --trgsubject Freesurfer --trglabel ./rh.BA45.label --hemi rh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA45.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./rh.BA45.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 5355 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 5355 nlabel points Performing mapping from target back to the source label 97884 Number of reverse mapping hits = 435 Checking for and removing duplicates Writing label file ./rh.BA45.label 5790 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.V1.label --trgsubject Freesurfer --trglabel ./rh.V1.label --hemi rh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.V1.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./rh.V1.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 4727 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 4727 nlabel points Performing mapping from target back to the source label 97884 Number of reverse mapping hits = 903 Checking for and removing duplicates Writing label file ./rh.V1.label 5630 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.V2.label --trgsubject Freesurfer --trglabel ./rh.V2.label --hemi rh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.V2.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./rh.V2.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 8016 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 8016 nlabel points Performing mapping from target back to the source label 97884 Number of reverse mapping hits = 964 Checking for and removing duplicates Writing label file ./rh.V2.label 8980 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.MT.label --trgsubject Freesurfer --trglabel ./rh.MT.label --hemi rh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.MT.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./rh.MT.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 1932 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1932 nlabel points Performing mapping from target back to the source label 97884 Number of reverse mapping hits = 246 Checking for and removing duplicates Writing label file ./rh.MT.label 2178 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.perirhinal.label --trgsubject Freesurfer --trglabel ./rh.perirhinal.label --hemi rh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.perirhinal.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./rh.perirhinal.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 752 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 752 nlabel points Performing mapping from target back to the source label 97884 Number of reverse mapping hits = 17 Checking for and removing duplicates Writing label file ./rh.perirhinal.label 769 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA1.thresh.label --trgsubject Freesurfer --trglabel ./rh.BA1.thresh.label --hemi rh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA1.thresh.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./rh.BA1.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 876 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 876 nlabel points Performing mapping from target back to the source label 97884 Number of reverse mapping hits = 145 Checking for and removing duplicates Writing label file ./rh.BA1.thresh.label 1021 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA2.thresh.label --trgsubject Freesurfer --trglabel ./rh.BA2.thresh.label --hemi rh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA2.thresh.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./rh.BA2.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 2688 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2688 nlabel points Performing mapping from target back to the source label 97884 Number of reverse mapping hits = 344 Checking for and removing duplicates Writing label file ./rh.BA2.thresh.label 3032 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA3a.thresh.label --trgsubject Freesurfer --trglabel ./rh.BA3a.thresh.label --hemi rh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA3a.thresh.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./rh.BA3a.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 1698 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1698 nlabel points Performing mapping from target back to the source label 97884 Number of reverse mapping hits = 55 Checking for and removing duplicates Writing label file ./rh.BA3a.thresh.label 1753 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA3b.thresh.label --trgsubject Freesurfer --trglabel ./rh.BA3b.thresh.label --hemi rh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA3b.thresh.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./rh.BA3b.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 2183 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 2183 nlabel points Performing mapping from target back to the source label 97884 Number of reverse mapping hits = 96 Checking for and removing duplicates Writing label file ./rh.BA3b.thresh.label 2279 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA4a.thresh.label --trgsubject Freesurfer --trglabel ./rh.BA4a.thresh.label --hemi rh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA4a.thresh.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./rh.BA4a.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 1388 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1388 nlabel points Performing mapping from target back to the source label 97884 Number of reverse mapping hits = 24 Checking for and removing duplicates Writing label file ./rh.BA4a.thresh.label 1412 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA4p.thresh.label --trgsubject Freesurfer --trglabel ./rh.BA4p.thresh.label --hemi rh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA4p.thresh.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./rh.BA4p.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 1489 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1489 nlabel points Performing mapping from target back to the source label 97884 Number of reverse mapping hits = 12 Checking for and removing duplicates Writing label file ./rh.BA4p.thresh.label 1501 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA6.thresh.label --trgsubject Freesurfer --trglabel ./rh.BA6.thresh.label --hemi rh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA6.thresh.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./rh.BA6.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 6959 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 6959 nlabel points Performing mapping from target back to the source label 97884 Number of reverse mapping hits = 410 Checking for and removing duplicates Writing label file ./rh.BA6.thresh.label 7369 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA44.thresh.label --trgsubject Freesurfer --trglabel ./rh.BA44.thresh.label --hemi rh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA44.thresh.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./rh.BA44.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 1012 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1012 nlabel points Performing mapping from target back to the source label 97884 Number of reverse mapping hits = 31 Checking for and removing duplicates Writing label file ./rh.BA44.thresh.label 1043 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA45.thresh.label --trgsubject Freesurfer --trglabel ./rh.BA45.thresh.label --hemi rh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.BA45.thresh.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./rh.BA45.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 1178 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 1178 nlabel points Performing mapping from target back to the source label 97884 Number of reverse mapping hits = 80 Checking for and removing duplicates Writing label file ./rh.BA45.thresh.label 1258 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.V1.thresh.label --trgsubject Freesurfer --trglabel ./rh.V1.thresh.label --hemi rh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.V1.thresh.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./rh.V1.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 3232 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3232 nlabel points Performing mapping from target back to the source label 97884 Number of reverse mapping hits = 677 Checking for and removing duplicates Writing label file ./rh.V1.thresh.label 3909 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.V2.thresh.label --trgsubject Freesurfer --trglabel ./rh.V2.thresh.label --hemi rh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.V2.thresh.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./rh.V2.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 3437 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 3437 nlabel points Performing mapping from target back to the source label 97884 Number of reverse mapping hits = 457 Checking for and removing duplicates Writing label file ./rh.V2.thresh.label 3894 mri_label2label: Done mri_label2label --srcsubject fsaverage --srclabel /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.MT.thresh.label --trgsubject Freesurfer --trglabel ./rh.MT.thresh.label --hemi rh --regmethod surface srclabel = /tmp/surfaKCaG0free/MRI/fsaverage/label/rh.MT.thresh.label srcsubject = fsaverage trgsubject = Freesurfer trglabel = ./rh.MT.thresh.label regmethod = surface srchemi = rh trghemi = rh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /tmp/surfaKCaG0free/MRI FREESURFER_HOME /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 Loading source label. Found 268 points in source label. Starting surface-based mapping Reading source registration /tmp/surfaKCaG0free/MRI/fsaverage/surf/rh.sphere.reg Rescaling ... original radius = 100 Reading target surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white Reading target registration /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.sphere.reg Rescaling ... original radius = 100 Building target registration hash (res=16). Building source registration hash (res=16). INFO: found 268 nlabel points Performing mapping from target back to the source label 97884 Number of reverse mapping hits = 84 Checking for and removing duplicates Writing label file ./rh.MT.thresh.label 352 mri_label2label: Done mris_label2annot --s Freesurfer --hemi rh --ctab /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose Reading ctab /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /tmp/surfaKCaG0free/MRI/Freesurfer/label cmdline mris_label2annot --s Freesurfer --hemi rh --ctab /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/colortable_BA.txt --l rh.BA1.label --l rh.BA2.label --l rh.BA3a.label --l rh.BA3b.label --l rh.BA4a.label --l rh.BA4p.label --l rh.BA6.label --l rh.BA44.label --l rh.BA45.label --l rh.V1.label --l rh.V2.label --l rh.MT.label --l rh.perirhinal.label --a BA --maxstatwinner --noverbose sysname Linux hostname rc-russia machine x86_64 user rudolphpienaar subject Freesurfer hemi rh SUBJECTS_DIR /tmp/surfaKCaG0free/MRI ColorTable /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/colortable_BA.txt AnnotName BA nlables 13 LabelThresh 0 0.000000 Loading /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT 13 16422433 perirhinal Mapping unhit to unknown Found 67382 unhit vertices Writing annot to /tmp/surfaKCaG0free/MRI/Freesurfer/label/rh.BA.annot mris_label2annot --s Freesurfer --hemi rh --ctab /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose Reading ctab /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/colortable_BA.txt Number of ctab entries 14 $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /tmp/surfaKCaG0free/MRI/Freesurfer/label cmdline mris_label2annot --s Freesurfer --hemi rh --ctab /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/colortable_BA.txt --l rh.BA1.thresh.label --l rh.BA2.thresh.label --l rh.BA3a.thresh.label --l rh.BA3b.thresh.label --l rh.BA4a.thresh.label --l rh.BA4p.thresh.label --l rh.BA6.thresh.label --l rh.BA44.thresh.label --l rh.BA45.thresh.label --l rh.V1.thresh.label --l rh.V2.thresh.label --l rh.MT.thresh.label --a BA.thresh --maxstatwinner --noverbose sysname Linux hostname rc-russia machine x86_64 user rudolphpienaar subject Freesurfer hemi rh SUBJECTS_DIR /tmp/surfaKCaG0free/MRI ColorTable /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/colortable_BA.txt AnnotName BA.thresh nlables 12 LabelThresh 0 0.000000 Loading /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.orig 1 1530880 BA1 2 16749699 BA2 3 16711680 BA3a 4 3368703 BA3b 5 1376196 BA4a 6 13382655 BA4p 7 10036737 BA6 8 2490521 BA44 9 39283 BA45 10 3993 V1 11 8508928 V2 12 10027163 MT Mapping unhit to unknown Found 80511 unhit vertices Writing annot to /tmp/surfaKCaG0free/MRI/Freesurfer/label/rh.BA.thresh.annot mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab Freesurfer rh white computing statistics for each annotation in ./rh.BA.annot. reading volume /tmp/surfaKCaG0free/MRI/Freesurfer/mri/wm.mgz... reading input surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white... reading input pial surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.pial... reading input white surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/colortable_BA.txt) Saving annotation colortable ./BA.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 944 538 1788 2.321 0.650 0.197 0.149 94 5.5 BA1 3057 2042 5453 2.294 0.670 0.145 0.106 81 12.5 BA2 850 584 833 1.902 0.690 0.175 0.134 19 3.1 BA3a 1698 1121 2484 1.886 0.711 0.145 0.068 50 5.2 BA3b 982 664 2483 2.745 0.760 0.137 0.052 14 2.2 BA4a 718 492 1342 2.425 0.586 0.137 0.045 10 1.4 BA4p 6391 4194 17213 2.892 0.995 0.153 0.085 160 23.4 BA6 2399 1572 5402 2.741 0.738 0.149 0.071 51 7.2 BA44 3099 2088 8295 3.039 0.814 0.142 0.058 53 7.3 BA45 3163 2149 4714 1.962 0.624 0.161 0.115 264 16.8 V1 5244 3457 9122 2.298 0.757 0.171 0.129 184 30.4 V2 1539 1030 3442 2.798 0.661 0.140 0.113 31 10.3 MT 418 257 1642 3.931 0.479 0.135 0.086 6 1.4 perirhinal mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.thresh.annot -c ./BA.thresh.ctab Freesurfer rh white computing statistics for each annotation in ./rh.BA.thresh.annot. reading volume /tmp/surfaKCaG0free/MRI/Freesurfer/mri/wm.mgz... reading input surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white... reading input pial surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.pial... reading input white surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white... INFO: assuming MGZ format for volumes. reading colortable from annotation file... colortable with 14 entries read (originally /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3/average/colortable_BA.txt) Saving annotation colortable ./BA.thresh.ctab table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 615 351 1080 2.198 0.718 0.228 0.181 63 5.2 BA1 2003 1312 3818 2.360 0.670 0.136 0.067 34 4.2 BA2 701 485 636 1.793 0.626 0.174 0.146 16 2.5 BA3a 1348 956 1768 1.715 0.647 0.132 0.051 28 2.8 BA3b 635 426 1903 3.089 0.760 0.161 0.074 12 1.9 BA4a 642 440 1153 2.430 0.574 0.126 0.038 7 1.1 BA4p 4020 2640 10627 2.835 0.993 0.151 0.080 101 12.3 BA6 545 351 1521 3.076 0.590 0.146 0.061 12 1.4 BA44 746 500 2281 3.141 0.721 0.154 0.066 16 2.0 BA45 3006 2036 4344 1.946 0.605 0.159 0.116 259 16.2 V1 2826 1869 5165 2.328 0.739 0.170 0.114 101 15.3 V2 286 190 653 2.772 0.611 0.159 0.102 6 1.1 MT /tmp/surfaKCaG0free/MRI/Freesurfer/label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label lh Fri Mar 18 20:43:53 EDT 2016 mris_spherical_average -erode 1 -orig white -t 0.4 -o Freesurfer label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label painting output onto subject Freesurfer. processing subject lh.EC_average... reading output surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.sphere.reg... eroding label 1 times before writing thresholding label stat at 0.400 before writing only 1 subject - copying statistics... writing label with 719 points to lh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label Freesurfer lh white limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /tmp/surfaKCaG0free/MRI/Freesurfer/mri/wm.mgz... reading input surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white... reading input pial surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.pial... reading input white surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/lh.white... INFO: assuming MGZ format for volumes. table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 277 139 909 3.399 0.638 0.130 0.063 5 0.6 ./lh.entorhinal_exvivo.label #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Fri Mar 18 20:44:04 EDT 2016 mris_spherical_average -erode 1 -orig white -t 0.4 -o Freesurfer label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label painting output onto subject Freesurfer. processing subject rh.EC_average... reading output surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.sphere.reg... eroding label 1 times before writing thresholding label stat at 0.400 before writing only 1 subject - copying statistics... writing label with 596 points to rh.entorhinal_exvivo.label... mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label Freesurfer rh white limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /tmp/surfaKCaG0free/MRI/Freesurfer/mri/wm.mgz... reading input surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white... reading input pial surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.pial... reading input white surface /tmp/surfaKCaG0free/MRI/Freesurfer/surf/rh.white... INFO: assuming MGZ format for volumes. table columns are: number of vertices total surface area (mm^2) total gray matter volume (mm^3) average cortical thickness +- standard deviation (mm) integrated rectified mean curvature integrated rectified Gaussian curvature folding index intrinsic curvature index structure name 236 116 800 3.593 0.414 0.151 0.128 7 1.5 ./rh.entorhinal_exvivo.label #------------------------------------------ Started at Fri Mar 18 11:59:31 EDT 2016 Ended at Fri Mar 18 20:44:15 EDT 2016 #@#%# recon-all-run-time-hours 8.746 recon-all -s Freesurfer finished without error at Fri Mar 18 20:44:15 EDT 2016 \n\n New invocation of recon-all \n\n Thu Dec 20 12:02:59 EST 2018 /Users/emitakahashi/freesurfer/subjects/ASD001 /Applications/freesurfer/bin/recon-all -s ASD001 -qcache subjid ASD001 setenv SUBJECTS_DIR /Users/emitakahashi/freesurfer/subjects FREESURFER_HOME /Applications/freesurfer Actual FREESURFER_HOME /Applications/freesurfer build-stamp.txt: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Darwin emis-mbp.tch.harvard.edu 18.0.0 Darwin Kernel Version 18.0.0: Wed Aug 22 20:13:40 PDT 2018; root:xnu-4903.201.2~1/RELEASE_X86_64 x86_64 cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited descriptors 256 memorylocked unlimited maxproc 2837 PhysMem: 5361M used (2790M wired), 27G unused. ######################################## program versions used $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:02:59-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@gust.nmr.mgh.harvard.edu (x86_64-apple-darwin11.4.2) on 2015-06-19 at 15:37:08 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/12/20-17:03:00-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:01-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:01-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:01-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:01-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:01-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:01-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:01-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:01-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:01-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:01-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/12/20-17:03:01-GMT BuildTimeStamp: Jan 19 2017 22:24:12 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: emitakahashi Machine: emis-mbp.tch.harvard.edu Platform: Darwin PlatformVersion: 18.0.0 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /Applications/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /Applications/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer Previous: /neuro/arch/x86_64-Linux/packages/freesurfer/stable-5.3 #-------------------------------------------- #@# Qdec Cache preproc lh thickness fsaverage Thu Dec 20 12:03:02 EST 2018 /Users/emitakahashi/freesurfer/subjects/ASD001/surf \n mris_preproc --s ASD001 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh \n nsubjects = 1 tmpdir is ./tmp.mris_preproc.4502 /Users/emitakahashi/freesurfer/subjects/ASD001/surf Log file is lh.thickness.fsaverage.mris_preproc.log Thu Dec 20 12:03:02 EST 2018 setenv SUBJECTS_DIR /Users/emitakahashi/freesurfer/subjects cd /Users/emitakahashi/freesurfer/subjects/ASD001/surf /Applications/freesurfer/bin/mris_preproc --s ASD001 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh Darwin emis-mbp.tch.harvard.edu 18.0.0 Darwin Kernel Version 18.0.0: Wed Aug 22 20:13:40 PDT 2018; root:xnu-4903.201.2~1/RELEASE_X86_64 x86_64 $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.4502 Src lh sphere.reg Trg lh sphere.reg \n\n --------------------------------------------------- #@# 1/1 ASD001 Thu Dec 20 12:03:02 EST 2018 -------------- ----------------------- mri_surf2surf --srcsubject ASD001 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.4502/ASD001.1.mgh --sval /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.thickness --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /Users/emitakahashi/freesurfer/subjects cd /Users/emitakahashi/freesurfer/subjects/ASD001/surf mri_surf2surf --srcsubject ASD001 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.4502/ASD001.1.mgh --sval /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.thickness --sfmt curv --noreshape --cortex sysname Darwin hostname emis-mbp.tch.harvard.edu machine x86_64 user emitakahashi srcsubject = ASD001 srcval = /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.thickness srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.4502/ASD001.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.sphere.reg Loading source data Reading curvature file /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.thickness Reading source subject label mask lh.cortex.label masking the input Reading target surface reg /Users/emitakahashi/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (94903) Reverse Loop had 11512 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 156095, nTrgMulti = 7747, MnTrgMultiHits = 2.48599 nSrc121 = 49256, nSrcLost = 0, nSrcMulti = 45647, MnSrcMultiHits = 2.76246 Reading target space mask label lh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.4502/ASD001.1.mgh \n\n ----------------------- mri_concat ./tmp.mris_preproc.4502/ASD001.1.mgh --o lh.thickness.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.thickness.fsaverage.mgh \n\n Cleaning up ----------------------- rm -r ./tmp.mris_preproc.4502 Thu Dec 20 12:03:05 EST 2018 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc lh area fsaverage Thu Dec 20 12:03:05 EST 2018 /Users/emitakahashi/freesurfer/subjects/ASD001/surf \n mris_preproc --s ASD001 --hemi lh --meas area --target fsaverage --out lh.area.fsaverage.mgh \n nsubjects = 1 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.4632 /Users/emitakahashi/freesurfer/subjects/ASD001/surf Log file is lh.area.fsaverage.mris_preproc.log Thu Dec 20 12:03:06 EST 2018 setenv SUBJECTS_DIR /Users/emitakahashi/freesurfer/subjects cd /Users/emitakahashi/freesurfer/subjects/ASD001/surf /Applications/freesurfer/bin/mris_preproc --s ASD001 --hemi lh --meas area --target fsaverage --out lh.area.fsaverage.mgh Darwin emis-mbp.tch.harvard.edu 18.0.0 Darwin Kernel Version 18.0.0: Wed Aug 22 20:13:40 PDT 2018; root:xnu-4903.201.2~1/RELEASE_X86_64 x86_64 $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.4632 Src lh sphere.reg Trg lh sphere.reg \n\n --------------------------------------------------- #@# 1/1 ASD001 Thu Dec 20 12:03:06 EST 2018 -------------- ----------------------- mri_surf2surf --srcsubject ASD001 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.4632/ASD001.1.mgh --sval /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.area --jac --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /Users/emitakahashi/freesurfer/subjects cd /Users/emitakahashi/freesurfer/subjects/ASD001/surf mri_surf2surf --srcsubject ASD001 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.4632/ASD001.1.mgh --sval /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.area --jac --sfmt curv --noreshape --cortex sysname Darwin hostname emis-mbp.tch.harvard.edu machine x86_64 user emitakahashi srcsubject = ASD001 srcval = /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.area srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.4632/ASD001.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.sphere.reg Loading source data Reading curvature file /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.area Reading source subject label mask lh.cortex.label masking the input Reading target surface reg /Users/emitakahashi/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr_jac: building source hash (res=16). Surf2SurfJac: 1st Forward Loop (163842) Surf2SurfJac: 2nd Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2SurfJac: Reverse Loop (94903) Reverse Loop had 11512 hits INFO: nSrcLost = 0 surf2surf_nnfr_jac() done nTrg121 = 156095, nTrgMulti = 7747, MnTrgMultiHits = 2.48599 nSrc121 = 49256, nSrcLost = 0, nSrcMulti = 45647, MnSrcMultiHits = 2.76246 Reading target space mask label lh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.4632/ASD001.1.mgh \n\n ----------------------- mri_concat ./tmp.mris_preproc.4632/ASD001.1.mgh --o lh.area.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.area.fsaverage.mgh \n\n Cleaning up ----------------------- rm -r ./tmp.mris_preproc.4632 Thu Dec 20 12:03:10 EST 2018 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc lh area.pial fsaverage Thu Dec 20 12:03:10 EST 2018 /Users/emitakahashi/freesurfer/subjects/ASD001/surf \n mris_preproc --s ASD001 --hemi lh --meas area.pial --target fsaverage --out lh.area.pial.fsaverage.mgh \n nsubjects = 1 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.4762 /Users/emitakahashi/freesurfer/subjects/ASD001/surf Log file is lh.area.pial.fsaverage.mris_preproc.log Thu Dec 20 12:03:10 EST 2018 setenv SUBJECTS_DIR /Users/emitakahashi/freesurfer/subjects cd /Users/emitakahashi/freesurfer/subjects/ASD001/surf /Applications/freesurfer/bin/mris_preproc --s ASD001 --hemi lh --meas area.pial --target fsaverage --out lh.area.pial.fsaverage.mgh Darwin emis-mbp.tch.harvard.edu 18.0.0 Darwin Kernel Version 18.0.0: Wed Aug 22 20:13:40 PDT 2018; root:xnu-4903.201.2~1/RELEASE_X86_64 x86_64 $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.4762 Src lh sphere.reg Trg lh sphere.reg \n\n --------------------------------------------------- #@# 1/1 ASD001 Thu Dec 20 12:03:10 EST 2018 -------------- ----------------------- mri_surf2surf --srcsubject ASD001 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.4762/ASD001.1.mgh --sval /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.area.pial --jac --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /Users/emitakahashi/freesurfer/subjects cd /Users/emitakahashi/freesurfer/subjects/ASD001/surf mri_surf2surf --srcsubject ASD001 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.4762/ASD001.1.mgh --sval /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.area.pial --jac --sfmt curv --noreshape --cortex sysname Darwin hostname emis-mbp.tch.harvard.edu machine x86_64 user emitakahashi srcsubject = ASD001 srcval = /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.area.pial srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.4762/ASD001.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.sphere.reg Loading source data Reading curvature file /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.area.pial Reading source subject label mask lh.cortex.label masking the input Reading target surface reg /Users/emitakahashi/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr_jac: building source hash (res=16). Surf2SurfJac: 1st Forward Loop (163842) Surf2SurfJac: 2nd Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2SurfJac: Reverse Loop (94903) Reverse Loop had 11512 hits INFO: nSrcLost = 0 surf2surf_nnfr_jac() done nTrg121 = 156095, nTrgMulti = 7747, MnTrgMultiHits = 2.48599 nSrc121 = 49256, nSrcLost = 0, nSrcMulti = 45647, MnSrcMultiHits = 2.76246 Reading target space mask label lh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.4762/ASD001.1.mgh \n\n ----------------------- mri_concat ./tmp.mris_preproc.4762/ASD001.1.mgh --o lh.area.pial.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.area.pial.fsaverage.mgh \n\n Cleaning up ----------------------- rm -r ./tmp.mris_preproc.4762 Thu Dec 20 12:03:14 EST 2018 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc lh volume fsaverage Thu Dec 20 12:03:14 EST 2018 /Users/emitakahashi/freesurfer/subjects/ASD001/surf \n mris_preproc --s ASD001 --hemi lh --meas volume --target fsaverage --out lh.volume.fsaverage.mgh \n nsubjects = 1 INFO: turning on jacobican correction tmpdir is ./tmp.mris_preproc.4891 /Users/emitakahashi/freesurfer/subjects/ASD001/surf Log file is lh.volume.fsaverage.mris_preproc.log Thu Dec 20 12:03:14 EST 2018 setenv SUBJECTS_DIR /Users/emitakahashi/freesurfer/subjects cd /Users/emitakahashi/freesurfer/subjects/ASD001/surf /Applications/freesurfer/bin/mris_preproc --s ASD001 --hemi lh --meas volume --target fsaverage --out lh.volume.fsaverage.mgh Darwin emis-mbp.tch.harvard.edu 18.0.0 Darwin Kernel Version 18.0.0: Wed Aug 22 20:13:40 PDT 2018; root:xnu-4903.201.2~1/RELEASE_X86_64 x86_64 $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.4891 Src lh sphere.reg Trg lh sphere.reg \n\n --------------------------------------------------- #@# 1/1 ASD001 Thu Dec 20 12:03:14 EST 2018 -------------- ----------------------- mri_surf2surf --srcsubject ASD001 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.4891/ASD001.1.mgh --sval /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.volume --jac --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /Users/emitakahashi/freesurfer/subjects cd /Users/emitakahashi/freesurfer/subjects/ASD001/surf mri_surf2surf --srcsubject ASD001 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.4891/ASD001.1.mgh --sval /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.volume --jac --sfmt curv --noreshape --cortex sysname Darwin hostname emis-mbp.tch.harvard.edu machine x86_64 user emitakahashi srcsubject = ASD001 srcval = /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.volume srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.4891/ASD001.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.sphere.reg Loading source data Reading curvature file /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.volume Reading source subject label mask lh.cortex.label masking the input Reading target surface reg /Users/emitakahashi/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface with Jacobian Correction surf2surf_nnfr_jac: building source hash (res=16). Surf2SurfJac: 1st Forward Loop (163842) Surf2SurfJac: 2nd Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2SurfJac: Reverse Loop (94903) Reverse Loop had 11512 hits INFO: nSrcLost = 0 surf2surf_nnfr_jac() done nTrg121 = 156095, nTrgMulti = 7747, MnTrgMultiHits = 2.48599 nSrc121 = 49256, nSrcLost = 0, nSrcMulti = 45647, MnSrcMultiHits = 2.76246 Reading target space mask label lh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.4891/ASD001.1.mgh \n\n ----------------------- mri_concat ./tmp.mris_preproc.4891/ASD001.1.mgh --o lh.volume.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.volume.fsaverage.mgh \n\n Cleaning up ----------------------- rm -r ./tmp.mris_preproc.4891 Thu Dec 20 12:03:18 EST 2018 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc lh curv fsaverage Thu Dec 20 12:03:18 EST 2018 /Users/emitakahashi/freesurfer/subjects/ASD001/surf \n mris_preproc --s ASD001 --hemi lh --meas curv --target fsaverage --out lh.curv.fsaverage.mgh \n nsubjects = 1 tmpdir is ./tmp.mris_preproc.5020 /Users/emitakahashi/freesurfer/subjects/ASD001/surf Log file is lh.curv.fsaverage.mris_preproc.log Thu Dec 20 12:03:18 EST 2018 setenv SUBJECTS_DIR /Users/emitakahashi/freesurfer/subjects cd /Users/emitakahashi/freesurfer/subjects/ASD001/surf /Applications/freesurfer/bin/mris_preproc --s ASD001 --hemi lh --meas curv --target fsaverage --out lh.curv.fsaverage.mgh Darwin emis-mbp.tch.harvard.edu 18.0.0 Darwin Kernel Version 18.0.0: Wed Aug 22 20:13:40 PDT 2018; root:xnu-4903.201.2~1/RELEASE_X86_64 x86_64 $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.5020 Src lh sphere.reg Trg lh sphere.reg \n\n --------------------------------------------------- #@# 1/1 ASD001 Thu Dec 20 12:03:18 EST 2018 -------------- ----------------------- mri_surf2surf --srcsubject ASD001 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.5020/ASD001.1.mgh --sval /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.curv --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /Users/emitakahashi/freesurfer/subjects cd /Users/emitakahashi/freesurfer/subjects/ASD001/surf mri_surf2surf --srcsubject ASD001 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.5020/ASD001.1.mgh --sval /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.curv --sfmt curv --noreshape --cortex sysname Darwin hostname emis-mbp.tch.harvard.edu machine x86_64 user emitakahashi srcsubject = ASD001 srcval = /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.curv srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.5020/ASD001.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.sphere.reg Loading source data Reading curvature file /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.curv Reading source subject label mask lh.cortex.label masking the input Reading target surface reg /Users/emitakahashi/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (94903) Reverse Loop had 11512 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 156095, nTrgMulti = 7747, MnTrgMultiHits = 2.48599 nSrc121 = 49256, nSrcLost = 0, nSrcMulti = 45647, MnSrcMultiHits = 2.76246 Reading target space mask label lh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.5020/ASD001.1.mgh \n\n ----------------------- mri_concat ./tmp.mris_preproc.5020/ASD001.1.mgh --o lh.curv.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.curv.fsaverage.mgh \n\n Cleaning up ----------------------- rm -r ./tmp.mris_preproc.5020 Thu Dec 20 12:03:21 EST 2018 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc lh sulc fsaverage Thu Dec 20 12:03:21 EST 2018 /Users/emitakahashi/freesurfer/subjects/ASD001/surf \n mris_preproc --s ASD001 --hemi lh --meas sulc --target fsaverage --out lh.sulc.fsaverage.mgh \n nsubjects = 1 tmpdir is ./tmp.mris_preproc.5149 /Users/emitakahashi/freesurfer/subjects/ASD001/surf Log file is lh.sulc.fsaverage.mris_preproc.log Thu Dec 20 12:03:22 EST 2018 setenv SUBJECTS_DIR /Users/emitakahashi/freesurfer/subjects cd /Users/emitakahashi/freesurfer/subjects/ASD001/surf /Applications/freesurfer/bin/mris_preproc --s ASD001 --hemi lh --meas sulc --target fsaverage --out lh.sulc.fsaverage.mgh Darwin emis-mbp.tch.harvard.edu 18.0.0 Darwin Kernel Version 18.0.0: Wed Aug 22 20:13:40 PDT 2018; root:xnu-4903.201.2~1/RELEASE_X86_64 x86_64 $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c tmpdir is ./tmp.mris_preproc.5149 Src lh sphere.reg Trg lh sphere.reg \n\n --------------------------------------------------- #@# 1/1 ASD001 Thu Dec 20 12:03:22 EST 2018 -------------- ----------------------- mri_surf2surf --srcsubject ASD001 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.5149/ASD001.1.mgh --sval /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.sulc --sfmt curv --noreshape --cortex Source registration surface changed to sphere.reg Target registration surface changed to sphere.reg $Id: mri_surf2surf.c,v 1.103 2015/11/05 22:07:33 greve Exp $ setenv SUBJECTS_DIR /Users/emitakahashi/freesurfer/subjects cd /Users/emitakahashi/freesurfer/subjects/ASD001/surf mri_surf2surf --srcsubject ASD001 --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.5149/ASD001.1.mgh --sval /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.sulc --sfmt curv --noreshape --cortex sysname Darwin hostname emis-mbp.tch.harvard.edu machine x86_64 user emitakahashi srcsubject = ASD001 srcval = /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.sulc srctype = curv trgsubject = fsaverage trgval = ./tmp.mris_preproc.5149/ASD001.1.mgh trgtype = srcsurfreg = sphere.reg trgsurfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0 fwhm-out = 0 label-src = lh.cortex.label label-trg = lh.cortex.label OKToRevFaceOrder = 1 UseDualHemi = 0 Reading source surface reg /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.sphere.reg Loading source data Reading curvature file /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.sulc Reading source subject label mask lh.cortex.label masking the input Reading target surface reg /Users/emitakahashi/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Done Using surf2surf_nnfr() Mapping Source Volume onto Source Subject Surface surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (94903) Reverse Loop had 11512 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 nTrg121 = 156095, nTrgMulti = 7747, MnTrgMultiHits = 2.48599 nSrc121 = 49256, nSrcLost = 0, nSrcMulti = 45647, MnSrcMultiHits = 2.76246 Reading target space mask label lh.cortex.label masking the input Saving target data Saving to ./tmp.mris_preproc.5149/ASD001.1.mgh \n\n ----------------------- mri_concat ./tmp.mris_preproc.5149/ASD001.1.mgh --o lh.sulc.fsaverage.mgh ninputs = 1 Checking inputs nframestot = 1 Allocing output Done allocing nframes = 1 Writing to lh.sulc.fsaverage.mgh \n\n Cleaning up ----------------------- rm -r ./tmp.mris_preproc.5149 Thu Dec 20 12:03:25 EST 2018 mris_preproc done #-------------------------------------------- #@# Qdec Cache preproc lh white.K fsaverage Thu Dec 20 12:03:25 EST 2018 /Users/emitakahashi/freesurfer/subjects/ASD001/surf \n mris_preproc --s ASD001 --hemi lh --meas white.K --target fsaverage --out lh.white.K.fsaverage.mgh \n nsubjects = 1 ERROR: cannot find /Users/emitakahashi/freesurfer/subjects/ASD001/surf/lh.white.K Darwin emis-mbp.tch.harvard.edu 18.0.0 Darwin Kernel Version 18.0.0: Wed Aug 22 20:13:40 PDT 2018; root:xnu-4903.201.2~1/RELEASE_X86_64 x86_64 recon-all -s ASD001 exited with ERRORS at Thu Dec 20 12:03:25 EST 2018 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting