Wed Jul 11 14:04:48 CEST 2012 /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04 /opt/freesurfer/bin/recon-all -i /mnt/bp11dat/Studie43_Phantom_Arm/Rohdaten/P04/PT_3post/highres1/Jahn^Rainer-0002-0001-00004.dcm -i /mnt/bp11dat/Studie43_Phantom_Arm/Rohdaten/P04/PT_3post/highres2/Jahn^Rainer-0142-0001-00335.dcm -s PTpost_P04 subjid PTpost_P04 setenv SUBJECTS_DIR /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /srv/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Linux castor 2.6.34.10-0.6-default #1 SMP 2011-12-13 18:27:38 +0100 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse 13995420 kbytes vmemoryuse 53443920 kbytes descriptors 1024 memorylocked 64 kbytes maxproc 128526 total used free shared buffers cached Mem: 16465172 15909592 555580 0 272660 14550356 -/+ buffers/cache: 1086576 15378596 Swap: 50339640 10884 50328756 ######################################## program versions used $Id: recon-all,v 1.313.2.6 2010/08/04 15:50:56 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.10.2.1 2010/08/04 15:50:56 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:48-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.7 2010/02/07 22:50:52 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:48-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: tkregister2.c,v 1.117.2.1 2010/08/02 17:42:03 greve Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 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_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:49-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_normalize.c,v 1.65 2010/01/11 17:15:27 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:49-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_watershed.cpp,v 1.81.2.1 2010/06/17 21:41:28 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:49-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_gcut.cpp,v 1.7 2010/02/18 19:50:06 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:49-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_segment.c,v 1.35 2007/11/21 04:38:06 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:49-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_label2label.c,v 1.39 2010/03/27 21:24:31 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:49-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_em_register.c,v 1.77 2010/02/12 19:43:30 rge21 Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:49-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_ca_normalize.c,v 1.49 2010/04/23 18:17:44 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:49-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_ca_register.c,v 1.71 2010/06/14 21:28:03 mreuter Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:49-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_ca_label.c,v 1.92 2009/11/19 18:04:13 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:50-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_pretess.c,v 1.16.4.1 2010/07/02 17:30:23 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:50-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_fill.c,v 1.113 2009/11/19 19:07:00 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:50-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_tessellate.c,v 1.33 2010/05/03 16:57:06 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:50-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_concatenate_lta.c,v 1.5 2009/05/06 23:01:36 mreuter Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:50-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_normalize_tp2.c,v 1.6 2007/01/08 18:10:12 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:50-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_smooth.c,v 1.25 2010/03/04 15:40:29 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:50-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_inflate.c,v 1.40 2010/05/27 21:35:00 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:50-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_curvature.c,v 1.28 2008/11/13 18:49:41 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:50-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_sphere.c,v 1.54 2010/04/14 15:16:23 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:50-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_fix_topology.c,v 1.44 2010/05/27 23:37:16 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:51-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_topo_fixer.cpp,v 1.28 2007/11/27 18:37:19 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:51-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_ca_label.c,v 1.32 2010/03/27 00:59:09 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:51-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:51-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_make_surfaces.c,v 1.113 2010/04/08 19:42:02 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:51-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:51-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_volmask.cpp,v 1.22 2010/02/17 22:51:19 krish Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:51-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_anatomical_stats.c,v 1.68 2010/05/28 20:36:45 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:51-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:51-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_curvature_stats.c,v 1.60 2010/02/27 01:49:33 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:52-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_calc.c,v 1.28 2010/04/12 21:05:24 greve Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.31.2.1 2010/07/22 18:00:15 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:52-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_robust_register.cpp,v 1.31.2.1 2010/07/22 18:00:15 mreuter Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.18.2.3 2010/07/22 18:00:15 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:52-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_robust_template.cpp,v 1.18.2.3 2010/07/22 18:00:15 mreuter Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:52-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_and.c,v 1.3 2009/06/09 19:32:31 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:52-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_or.c,v 1.1 2009/06/09 19:32:31 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:52-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_fuse_segmentations.c,v 1.6 2009/06/10 18:59:24 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/11-12:04:52-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /opt/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04 mri_convert /mnt/bp11dat/Studie43_Phantom_Arm/Rohdaten/P04/PT_3post/highres1/Jahn^Rainer-0002-0001-00004.dcm /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001.mgz mri_convert /mnt/bp11dat/Studie43_Phantom_Arm/Rohdaten/P04/PT_3post/highres1/Jahn^Rainer-0002-0001-00004.dcm /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /mnt/bp11dat/Studie43_Phantom_Arm/Rohdaten/P04/PT_3post/highres1/Jahn^Rainer-0002-0001-00004.dcm... Getting Series No INFO: Found 194 files in /mnt/bp11dat/Studie43_Phantom_Arm/Rohdaten/P04/PT_3post/highres1 INFO: Scanning for Series Number 2 Scanning Directory INFO: found 192 files in series INFO: loading series header info. RunNo = 1 INFO: sorting. WARNING: file /mnt/bp11dat/Studie43_Phantom_Arm/Rohdaten/P04/PT_3post/highres1/Jahn^Rainer-0002-0001-00004.dcm does not contain a Siemens ASCII header has this file been anonymized? Proceeding as best as I can ... INFO: (256 256 192), nframes = 1, ismosaic=0 PE Dir ROW ROW FileName /mnt/bp11dat/Studie43_Phantom_Arm/Rohdaten/P04/PT_3post/highres1/Jahn^Rainer-0002-0001-00004.dcm Identification NumarisVer VB33D ScannerModel MAGNETOM VISION PatientName Jahn^Rainer Date and time StudyDate 20071106 StudyTime 132048.064000 SeriesTime 132250.551000 AcqTime 132252.550000 Acquisition parameters PulseSeq fl3d Protocol unknown PhEncDir ROW EchoNo 1 FlipAngle 30 EchoTime 5 InversionTime -1 RepetitionTime 15 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 1 SeriesNo 2 ImageNo 4 NImageRows 256 NImageCols 256 NFrames 1 SliceArraylSize 0 IsMosaic 0 ImgPos 99.2290 137.6869 121.2486 VolRes 1.0000 1.0000 1.0000 VolDim 256 256 192 Vc -0.0000 -1.0000 -0.0000 Vr -0.0000 0.0000 -1.0000 Vs -1.0000 0.0000 0.0000 VolCenter 3.2290 9.6869 -6.7514 TransferSyntaxUID unknown INFO: no Siemens slice order reversal detected (good!). TR=15.00, TE=5.00, TI=-1.00, flip angle=30.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001.mgz... /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04 mri_convert /mnt/bp11dat/Studie43_Phantom_Arm/Rohdaten/P04/PT_3post/highres2/Jahn^Rainer-0142-0001-00335.dcm /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002.mgz mri_convert /mnt/bp11dat/Studie43_Phantom_Arm/Rohdaten/P04/PT_3post/highres2/Jahn^Rainer-0142-0001-00335.dcm /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /mnt/bp11dat/Studie43_Phantom_Arm/Rohdaten/P04/PT_3post/highres2/Jahn^Rainer-0142-0001-00335.dcm... Getting Series No INFO: Found 194 files in /mnt/bp11dat/Studie43_Phantom_Arm/Rohdaten/P04/PT_3post/highres2 INFO: Scanning for Series Number 142 Scanning Directory INFO: found 192 files in series INFO: loading series header info. RunNo = 141 INFO: sorting. WARNING: file /mnt/bp11dat/Studie43_Phantom_Arm/Rohdaten/P04/PT_3post/highres2/Jahn^Rainer-0142-0001-00335.dcm does not contain a Siemens ASCII header has this file been anonymized? Proceeding as best as I can ... INFO: (256 256 192), nframes = 1, ismosaic=0 PE Dir ROW ROW FileName /mnt/bp11dat/Studie43_Phantom_Arm/Rohdaten/P04/PT_3post/highres2/Jahn^Rainer-0142-0001-00335.dcm Identification NumarisVer VB33D ScannerModel MAGNETOM VISION PatientName Jahn^Rainer Date and time StudyDate 20071106 StudyTime 132048.064000 SeriesTime 134935.461000 AcqTime 134936.930000 Acquisition parameters PulseSeq fl3d Protocol unknown PhEncDir ROW EchoNo 1 FlipAngle 30 EchoTime 5 InversionTime -1 RepetitionTime 15 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 141 SeriesNo 142 ImageNo 335 NImageRows 256 NImageCols 256 NFrames 1 SliceArraylSize 0 IsMosaic 0 ImgPos 99.2290 137.6869 121.2486 VolRes 1.0000 1.0000 1.0000 VolDim 256 256 192 Vc -0.0000 -1.0000 -0.0000 Vr -0.0000 0.0000 -1.0000 Vs -1.0000 0.0000 0.0000 VolCenter 3.2290 9.6869 -6.7514 TransferSyntaxUID unknown INFO: no Siemens slice order reversal detected (good!). TR=15.00, TE=5.00, TI=-1.00, flip angle=30.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002.mgz... #------------------------------------------ recon-all -s PTpost_P04 finished without error at Wed Jul 11 14:08:00 CEST 2012 New invocation of recon-all Mon Jul 16 12:57:59 CEST 2012 /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04 /opt/freesurfer/bin/recon-all -autorecon1 -s PTpost_P04 -no-isrunning subjid PTpost_P04 setenv SUBJECTS_DIR /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /srv/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Linux castor 2.6.34.10-0.6-default #1 SMP 2011-12-13 18:27:38 +0100 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse 13995420 kbytes vmemoryuse 53443920 kbytes descriptors 1024 memorylocked 64 kbytes maxproc 128526 total used free shared buffers cached Mem: 16465172 16293228 171944 0 254008 11931424 -/+ buffers/cache: 4107796 12357376 Swap: 50339640 145508 50194132 ######################################## program versions used $Id: recon-all,v 1.313.2.6 2010/08/04 15:50:56 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.10.2.1 2010/08/04 15:50:56 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:57:59-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.7 2010/02/07 22:50:52 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:00-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: tkregister2.c,v 1.117.2.1 2010/08/02 17:42:03 greve Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 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_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:00-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_normalize.c,v 1.65 2010/01/11 17:15:27 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:00-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_watershed.cpp,v 1.81.2.1 2010/06/17 21:41:28 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:00-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_gcut.cpp,v 1.7 2010/02/18 19:50:06 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:00-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_segment.c,v 1.35 2007/11/21 04:38:06 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:00-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_label2label.c,v 1.39 2010/03/27 21:24:31 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:00-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_em_register.c,v 1.77 2010/02/12 19:43:30 rge21 Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:01-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_ca_normalize.c,v 1.49 2010/04/23 18:17:44 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:01-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_ca_register.c,v 1.71 2010/06/14 21:28:03 mreuter Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:01-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_ca_label.c,v 1.92 2009/11/19 18:04:13 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:01-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_pretess.c,v 1.16.4.1 2010/07/02 17:30:23 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:01-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_fill.c,v 1.113 2009/11/19 19:07:00 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:01-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_tessellate.c,v 1.33 2010/05/03 16:57:06 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:01-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_concatenate_lta.c,v 1.5 2009/05/06 23:01:36 mreuter Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:02-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_normalize_tp2.c,v 1.6 2007/01/08 18:10:12 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:02-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_smooth.c,v 1.25 2010/03/04 15:40:29 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:02-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_inflate.c,v 1.40 2010/05/27 21:35:00 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:02-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_curvature.c,v 1.28 2008/11/13 18:49:41 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:02-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_sphere.c,v 1.54 2010/04/14 15:16:23 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:02-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_fix_topology.c,v 1.44 2010/05/27 23:37:16 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:02-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_topo_fixer.cpp,v 1.28 2007/11/27 18:37:19 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:02-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_ca_label.c,v 1.32 2010/03/27 00:59:09 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:03-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:03-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_make_surfaces.c,v 1.113 2010/04/08 19:42:02 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:03-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:03-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_volmask.cpp,v 1.22 2010/02/17 22:51:19 krish Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:03-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_anatomical_stats.c,v 1.68 2010/05/28 20:36:45 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:03-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:03-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_curvature_stats.c,v 1.60 2010/02/27 01:49:33 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:04-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_calc.c,v 1.28 2010/04/12 21:05:24 greve Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.31.2.1 2010/07/22 18:00:15 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:04-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_robust_register.cpp,v 1.31.2.1 2010/07/22 18:00:15 mreuter Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.18.2.3 2010/07/22 18:00:15 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:04-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_robust_template.cpp,v 1.18.2.3 2010/07/22 18:00:15 mreuter Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:04-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_and.c,v 1.3 2009/06/09 19:32:31 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:04-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_or.c,v 1.1 2009/06/09 19:32:31 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:04-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_fuse_segmentations.c,v 1.6 2009/06/10 18:59:24 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-10:58:04-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /opt/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Mon Jul 16 12:58:04 CEST 2012 Found 2 runs /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001.mgz /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002.mgz /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04 mri_robust_template --mov /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001.mgz /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002.mgz --average 1 --template /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --subsample 200 mri_robust_template logfile is /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/mri_robust_template.log /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04 mri_convert /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/rawavg.mgz /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig.mgz --conform mri_convert /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/rawavg.mgz /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig.mgz --conform $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/rawavg.mgz... TR=15.00, TE=5.00, TI=-1.00, flip angle=30.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) Original Data has (1, 1, 1) mm size and (256, 256, 192) 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 /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig.mgz... mri_add_xform_to_header -c /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/transforms/talairach.xfm /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig.mgz /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Nu Intensity Correction Mon Jul 16 13:24:33 CEST 2012 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri /opt/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.12 2009/12/16 20:15:41 greve Exp $ Linux castor 2.6.34.10-0.6-default #1 SMP 2011-12-13 18:27:38 +0100 x86_64 x86_64 x86_64 GNU/Linux Mon Jul 16 13:24:33 CEST 2012 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.15360 /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.15360/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.15360/nu0.mnc -odt float $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from orig.mgz... TR=15.00, TE=5.00, TI=-1.00, flip angle=30.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.15360/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Jul 16 13:24:49 CEST 2012 nu_correct -clobber ./tmp.mri_nu_correct.mni.15360/nu0.mnc ./tmp.mri_nu_correct.mni.15360/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.15360/0/ [preisler@castor:/mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/] [2012-07-16 13:24:49] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.15360/0/ ./tmp.mri_nu_correct.mni.15360/nu0.mnc ./tmp.mri_nu_correct.mni.15360/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 30 CV of field change: 0.000981976 [preisler@castor:/mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/] [2012-07-16 13:25:42] running: /opt/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.15360/nu0.mnc ./tmp.mri_nu_correct.mni.15360/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Mon Jul 16 13:25:53 CEST 2012 nu_correct -clobber ./tmp.mri_nu_correct.mni.15360/nu1.mnc ./tmp.mri_nu_correct.mni.15360/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.15360/1/ [preisler@castor:/mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/] [2012-07-16 13:25:53] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.15360/1/ ./tmp.mri_nu_correct.mni.15360/nu1.mnc ./tmp.mri_nu_correct.mni.15360/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 23 CV of field change: 0.000955315 [preisler@castor:/mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/] [2012-07-16 13:26:36] running: /opt/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.15360/nu1.mnc ./tmp.mri_nu_correct.mni.15360/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.15360/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.15360/ones.mgz $Id: mri_binarize.c,v 1.23.2.1 2010/07/28 20:07:29 greve Exp $ cwd /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.15360/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.15360/ones.mgz sysname Linux hostname castor machine x86_64 user preisler input ./tmp.mri_nu_correct.mni.15360/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.15360/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.15360/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.15360/sum.junk --avgwf ./tmp.mri_nu_correct.mni.15360/input.mean.dat $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.15360/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.15360/sum.junk --avgwf ./tmp.mri_nu_correct.mni.15360/input.mean.dat sysname Linux hostname castor machine x86_64 user preisler Loading ./tmp.mri_nu_correct.mni.15360/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 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.15360/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.15360/ones.mgz --i ./tmp.mri_nu_correct.mni.15360/nu2.mnc --sum ./tmp.mri_nu_correct.mni.15360/sum.junk --avgwf ./tmp.mri_nu_correct.mni.15360/output.mean.dat $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.15360/ones.mgz --i ./tmp.mri_nu_correct.mni.15360/nu2.mnc --sum ./tmp.mri_nu_correct.mni.15360/sum.junk --avgwf ./tmp.mri_nu_correct.mni.15360/output.mean.dat sysname Linux hostname castor machine x86_64 user preisler Loading ./tmp.mri_nu_correct.mni.15360/ones.mgz Loading ./tmp.mri_nu_correct.mni.15360/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.15360/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.15360/nu2.mnc ./tmp.mri_nu_correct.mni.15360/nu2.mnc mul 1.02851541848773712225 Saving result to './tmp.mri_nu_correct.mni.15360/nu2.mnc' (type=3) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.15360/nu2.mnc nu.mgz --like orig.mgz --conform mri_convert ./tmp.mri_nu_correct.mni.15360/nu2.mnc nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from ./tmp.mri_nu_correct.mni.15360/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) Original Data has (1, 1, 1) mm size and (256, 256, 256) voxels. Data is conformed to 1 mm size and 256 voxels for all directions INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to nu.mgz... Mon Jul 16 13:30:28 CEST 2012 mri_nu_correct.mni done #-------------------------------------------- #@# Talairach Mon Jul 16 13:30:28 CEST 2012 /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Jul 16 13:32:59 CEST 2012 /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5979, pval=0.2817 >= threshold=0.0050) awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/transforms/talairach_avi.log TalAviQA: 0.98193 z-score: 0 #-------------------------------------------- #@# Intensity Normalization Mon Jul 16 13:32:59 CEST 2012 /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.067 0.036 -0.049 -0.942; -0.031 1.023 -0.054 -18.659; 0.048 0.069 1.087 -15.780; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to T1.mgz 3D bias adjustment took 7 minutes and 58 seconds. MRIsplineNormalize(): npeaks = 19 Starting OpenSpline(): npoints = 19 white matter peak found at 111 white matter peak found at 91 gm peak at 63 (63), valley at 0 (0) csf peak at 31, setting threshold to 52 white matter peak found at 111 white matter peak found at 91 gm peak at 63 (63), valley at 0 (0) csf peak at 31, setting threshold to 52 #-------------------------------------------- #@# Skull Stripping Mon Jul 16 13:41:01 CEST 2012 /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri mri_em_register -skull nu.mgz /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/opt/freesurfer/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=16.0 skull bounding box = (49, 20, 21) --> (209, 255, 219) using (102, 98, 120) as brain centroid... mean wm in atlas = 126, using box (82,69,96) --> (121, 127,144) to find MRI wm before smoothing, mri peak at 126 after smoothing, mri peak at 125, scaling input intensities by 1.008 scaling channel 0 by 1.008 initial log_p = -10393.7 ************************************************ First Search limited to translation only. ************************************************ Found translation: (-3.1, 16.8, -11.1): log p = -10316.8 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-10316.8, old_max_log_p =-10316.8 (thresh=-10306.5) 1.000 0.000 0.000 -3.125; 0.000 1.000 0.000 16.761; 0.000 0.000 1.000 -11.080; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 1 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-10309.4, old_max_log_p =-10316.8 (thresh=-10306.5) 1.050 -0.102 -0.069 9.208; 0.101 1.014 -0.007 4.972; 0.069 0.000 1.055 -28.269; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 2 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-10306.6, old_max_log_p =-10309.4 (thresh=-10299.1) 1.054 -0.084 -0.026 0.761; 0.081 1.015 -0.041 10.017; 0.029 0.037 1.060 -28.500; 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 1.05448 -0.08442 -0.02634 0.76102; 0.08135 1.01474 -0.04055 10.01700; 0.02950 0.03732 1.05956 -28.49994; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.05448 -0.08442 -0.02634 0.76102; 0.08135 1.01474 -0.04055 10.01700; 0.02950 0.03732 1.05956 -28.49994; 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: 005: -log(p) = 10306.6 tol 0.000010 Resulting transform: 1.054 -0.084 -0.026 0.761; 0.081 1.015 -0.041 10.017; 0.029 0.037 1.060 -28.500; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -10306.6 (old=-10393.7) transform before final EM align: 1.054 -0.084 -0.026 0.761; 0.081 1.015 -0.041 10.017; 0.029 0.037 1.060 -28.500; 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 1.05448 -0.08442 -0.02634 0.76102; 0.08135 1.01474 -0.04055 10.01700; 0.02950 0.03732 1.05956 -28.49994; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.05448 -0.08442 -0.02634 0.76102; 0.08135 1.01474 -0.04055 10.01700; 0.02950 0.03732 1.05956 -28.49994; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 007: -log(p) = 1144968.5 tol 0.000000 final transform: 1.054 -0.084 -0.026 0.761; 0.081 1.015 -0.041 10.017; 0.029 0.037 1.060 -28.500; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 81 minutes and 37 seconds. mri_watershed -T1 -brain_atlas /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=129 y=99 z=128 r=97 first estimation of the main basin volume: 3929420 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=160, y=80, z=99, Imax=255 CSF=18, 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=11534093155 voxels, voxel volume =1.000 = 11534093155 mmm3 = 11534093.312 cm3 done. PostAnalyze...Basin Prior 275 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=129,y=101, z=116, r=9849 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=3, CSF_intensity=12, CSF_MAX=32 , nb = 40752 RIGHT_CER CSF_MIN=3, CSF_intensity=11, CSF_MAX=46 , nb = 2304 LEFT_CER CSF_MIN=2, CSF_intensity=13, CSF_MAX=40 , nb = 2016 RIGHT_BRAIN CSF_MIN=3, CSF_intensity=13, CSF_MAX=31 , nb = 18270 LEFT_BRAIN CSF_MIN=4, CSF_intensity=12, CSF_MAX=30 , nb = 17640 OTHER CSF_MIN=6, CSF_intensity=13, CSF_MAX=35 , nb = 522 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 32, 36, 44, 75 after analyzing : 32, 41, 44, 49 RIGHT_CER before analyzing : 46, 47, 48, 81 after analyzing : 46, 47, 48, 55 LEFT_CER before analyzing : 40, 42, 46, 80 after analyzing : 40, 44, 46, 53 RIGHT_BRAIN before analyzing : 31, 36, 46, 76 after analyzing : 31, 42, 46, 50 LEFT_BRAIN before analyzing : 30, 35, 44, 75 after analyzing : 30, 41, 44, 49 OTHER before analyzing : 35, 28, 0, 95 after analyzing : 24, 28, 28, 44 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...67 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.009 curvature mean = 72.919, std = 6.229 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 5.26, sigma = 7.42 after rotation: sse = 5.26, sigma = 7.42 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 5.84, its var is 6.94 before Erosion-Dilatation 2.44% of inacurate vertices after Erosion-Dilatation 2.34% 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...38 iterations mri_strip_skull: done peeling brain Brain Size = 1806517 voxels, voxel volume = 1.000 mm3 = 1806517 mmm3 = 1806.517 cm3 ****************************** Saving brainmask.auto.mgz done mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz mghWrite: could not write 256 bytes to brainmask.auto.mgz reading mask... white mean: 106.050072 threshold set to: 106.050072*0.360000=38.178026 calculating weights... doing mincut... now doing maxflow, be patient... g-cut done! post-processing... post-processing done! masking... cp brainmask.auto.mgz brainmask.mgz cp: writing `brainmask.mgz': No space left on device Linux castor 2.6.34.10-0.6-default #1 SMP 2011-12-13 18:27:38 +0100 x86_64 x86_64 x86_64 GNU/Linux recon-all -s PTpost_P04 exited with ERRORS at Mon Jul 16 15:08:54 CEST 2012 New invocation of recon-all Mon Jul 16 15:58:20 CEST 2012 /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04 /opt/freesurfer/bin/recon-all -autorecon1 -s PTpost_P04 -no-isrunning subjid PTpost_P04 setenv SUBJECTS_DIR /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /srv/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 Linux castor 2.6.34.10-0.6-default #1 SMP 2011-12-13 18:27:38 +0100 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse 13995420 kbytes vmemoryuse 53443920 kbytes descriptors 1024 memorylocked 64 kbytes maxproc 128526 total used free shared buffers cached Mem: 16465172 16377916 87256 0 10124 9789252 -/+ buffers/cache: 6578540 9886632 Swap: 50339640 175436 50164204 ######################################## program versions used $Id: recon-all,v 1.313.2.6 2010/08/04 15:50:56 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.10.2.1 2010/08/04 15:50:56 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:20-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.7 2010/02/07 22:50:52 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:21-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: tkregister2.c,v 1.117.2.1 2010/08/02 17:42:03 greve Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 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_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:21-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_normalize.c,v 1.65 2010/01/11 17:15:27 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:21-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_watershed.cpp,v 1.81.2.1 2010/06/17 21:41:28 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:21-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_gcut.cpp,v 1.7 2010/02/18 19:50:06 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:21-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_segment.c,v 1.35 2007/11/21 04:38:06 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:22-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_label2label.c,v 1.39 2010/03/27 21:24:31 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:22-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_em_register.c,v 1.77 2010/02/12 19:43:30 rge21 Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:22-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_ca_normalize.c,v 1.49 2010/04/23 18:17:44 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:22-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_ca_register.c,v 1.71 2010/06/14 21:28:03 mreuter Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:22-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_ca_label.c,v 1.92 2009/11/19 18:04:13 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:22-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_pretess.c,v 1.16.4.1 2010/07/02 17:30:23 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:23-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_fill.c,v 1.113 2009/11/19 19:07:00 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:23-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_tessellate.c,v 1.33 2010/05/03 16:57:06 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:23-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_concatenate_lta.c,v 1.5 2009/05/06 23:01:36 mreuter Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:23-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_normalize_tp2.c,v 1.6 2007/01/08 18:10:12 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:23-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_smooth.c,v 1.25 2010/03/04 15:40:29 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:24-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_inflate.c,v 1.40 2010/05/27 21:35:00 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:24-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_curvature.c,v 1.28 2008/11/13 18:49:41 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:24-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_sphere.c,v 1.54 2010/04/14 15:16:23 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:24-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_fix_topology.c,v 1.44 2010/05/27 23:37:16 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:24-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_topo_fixer.cpp,v 1.28 2007/11/27 18:37:19 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:24-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_ca_label.c,v 1.32 2010/03/27 00:59:09 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:25-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:25-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_make_surfaces.c,v 1.113 2010/04/08 19:42:02 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:25-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_register.c,v 1.56 2010/02/28 23:08:04 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:25-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_volmask.cpp,v 1.22 2010/02/17 22:51:19 krish Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:25-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_anatomical_stats.c,v 1.68 2010/05/28 20:36:45 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:25-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:26-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_curvature_stats.c,v 1.60 2010/02/27 01:49:33 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:26-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mris_calc.c,v 1.28 2010/04/12 21:05:24 greve Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.31.2.1 2010/07/22 18:00:15 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:26-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_robust_register.cpp,v 1.31.2.1 2010/07/22 18:00:15 mreuter Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.18.2.3 2010/07/22 18:00:15 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:26-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_robust_template.cpp,v 1.18.2.3 2010/07/22 18:00:15 mreuter Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:26-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_and.c,v 1.3 2009/06/09 19:32:31 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:27-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_or.c,v 1.1 2009/06/09 19:32:31 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:27-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_fuse_segmentations.c,v 1.6 2009/06/10 18:59:24 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/16-13:58:27-GMT BuildTimeStamp: Aug 13 2010 15:52:37 CVS: $Id: mri_segstats.c,v 1.69.2.1 2010/07/26 16:19:29 greve Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /opt/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Mon Jul 16 15:58:27 CEST 2012 Found 2 runs /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001.mgz /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002.mgz /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04 mri_robust_template --mov /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001.mgz /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002.mgz --average 1 --template /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --subsample 200 mri_robust_template logfile is /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/mri_robust_template.log /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04 mri_convert /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/rawavg.mgz /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig.mgz --conform mri_convert /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/rawavg.mgz /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig.mgz --conform $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/rawavg.mgz... TR=15.00, TE=5.00, TI=-1.00, flip angle=30.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) Original Data has (1, 1, 1) mm size and (256, 256, 192) 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 /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig.mgz... mri_add_xform_to_header -c /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/transforms/talairach.xfm /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig.mgz /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Nu Intensity Correction Mon Jul 16 16:30:43 CEST 2012 mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri /opt/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.12 2009/12/16 20:15:41 greve Exp $ Linux castor 2.6.34.10-0.6-default #1 SMP 2011-12-13 18:27:38 +0100 x86_64 x86_64 x86_64 GNU/Linux Mon Jul 16 16:30:44 CEST 2012 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.16115 /mnt/bp11dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.16115/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.16115/nu0.mnc -odt float mri_convert: posixio.c:210: px_pgin: Assertion `*posp == ((off_t)(-1)) || *posp == lseek(nciop->fd, 0, 1)' failed. $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from orig.mgz... TR=15.00, TE=5.00, TI=-1.00, flip angle=30.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.16115/nu0.mnc... Abort ERROR: converting to minc Linux castor 2.6.34.10-0.6-default #1 SMP 2011-12-13 18:27:38 +0100 x86_64 x86_64 x86_64 GNU/Linux recon-all -s PTpost_P04 exited with ERRORS at Mon Jul 16 16:30:59 CEST 2012 New invocation of recon-all Thu Jul 26 14:39:38 CEST 2012 /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04 /opt/freesurfer/bin/recon-all -autorecon1 -s PTpost_P04 -no-isrunning subjid PTpost_P04 setenv SUBJECTS_DIR /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /srv/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux castor 2.6.34.10-0.6-default #1 SMP 2011-12-13 18:27:38 +0100 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse 13995420 kbytes vmemoryuse 53443920 kbytes descriptors 1024 memorylocked 64 kbytes maxproc 128526 total used free shared buffers cached Mem: 16465172 16353988 111184 0 169076 12302596 -/+ buffers/cache: 3882316 12582856 Swap: 50339640 1268 50338372 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 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: 2012/07/26-12:39:39-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:39-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 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: 2012/07/26-12:39:39-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:39-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:39-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:40-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:40-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:40-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:40-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:40-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:40-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:43-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:43-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:43-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:43-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:43-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:43-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:44-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:44-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:44-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:44-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:44-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:45-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:45-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:45-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-12:39:45-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /opt/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Thu Jul 26 14:39:45 CEST 2012 Found 2 runs /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001.mgz /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04 mri_robust_template --mov /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001.mgz /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002.mgz --average 1 --template /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001-iscale.txt /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002-iscale.txt --subsample 200 --lta /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001.lta /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002.lta $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ --mov: Using /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001.mgz as movable/source volume. --mov: Using /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001.mgz'... reading source '/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002.mgz'... MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002.mgz ) to TP 1 ( /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001.mgz ) Registration::setSourceAndTarget ... Mov: (1, 1, 1)mm and dim (256, 256, 192) Dst: (1, 1, 1)mm and dim (256, 256, 192) Asserting both images: 1mm isotropic and (256, 256, 192) voxels - no Source reslice necessary - no Target reslice necessary Registration::findSaturation - Gaussian Pyramid - Gaussian Pyramid - Max Resolution used: 2 -- gpS ( 64 , 64 , 48 ) -- gpT ( 64 , 64 , 48 ) - computing centroids - computing initial transform -- using translation info - running loop to estimate saturation parameter: -- Iteration: 1 trying sat: 16 min sat: 0 ( -1 ), max sat: 16 ( 0.0889289 ), sat diff: 16 -- Iteration: 2 trying sat: 8 min sat: 8 ( 0.229024 ), max sat: 16 ( 0.0889289 ), sat diff: 8 -- Iteration: 3 trying sat: 12 min sat: 8 ( 0.229024 ), max sat: 12 ( 0.13274 ), sat diff: 4 -- Iteration: 4 trying sat: 10 min sat: 8 ( 0.229024 ), max sat: 10 ( 0.171133 ), sat diff: 2 -- Iteration: 5 trying sat: 9 min sat: 9 ( 0.197016 ), max sat: 10 ( 0.171133 ), sat diff: 1 -- Iteration: 6 trying sat: 9.5 - final SAT: 10 ( it: 6 , weight check 0.171133 <= 0.175 ) Registration::computeMultiresRegistration - computing centroids - computing initial transform -- using translation info - initial transform: Ti = [ ... 1.0000000000000 0 0 -0.4110469447285 0 1.0000000000000 0 0.1530539910717 0 0 1.0000000000000 0.3546136792791 0 0 0 1.0000000000000 ] - initial iscale: Ii =1 Resolution: 3 S( 32 32 24 ) T( 32 32 24 ) Iteration(f): 1 -- diff. to prev. transform: 0.450062 Iteration(f): 2 -- diff. to prev. transform: 0.0557345 Iteration(f): 3 -- diff. to prev. transform: 0.00654747 < 0.01 :-) Resolution: 2 S( 64 64 48 ) T( 64 64 48 ) Iteration(f): 1 -- diff. to prev. transform: 0.31352 Iteration(f): 2 -- diff. to prev. transform: 0.0484814 Iteration(f): 3 -- diff. to prev. transform: 0.0134828 Iteration(f): 4 -- diff. to prev. transform: 0.007309 < 0.01 :-) Resolution: 1 S( 128 128 96 ) T( 128 128 96 ) Iteration(f): 1 -- diff. to prev. transform: 0.416278 Iteration(f): 2 -- diff. to prev. transform: 0.0296166 Iteration(f): 3 -- diff. to prev. transform: 0.0265161 Iteration(f): 4 -- diff. to prev. transform: 0.00248624 < 0.01 :-) Resolution: 0 S( 256 256 192 ) T( 256 256 192 ) Iteration(f): 1 (subsample 200) -- diff. to prev. transform: 0.155631 Iteration(f): 2 (subsample 200) -- diff. to prev. transform: 0.00229369 < 0.01 :-) - final transform: Tf = [ ... 0.9999468775282 -0.0102213656869 0.0013288359668 0.7743403778683 0.0102309703053 0.9999200283784 -0.0074339824001 -0.7249879574123 -0.0012527442450 0.0074471827699 0.9999714846438 -0.6657203299900 0 0 0 1.0000000000000 ] - final iscale: If = 1.00501 warping movs and creating initial template... allow intensity scaling using median Writing final template: /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/rawavg.mgz Writing final transforms (warps etc.)... Determinant( lta[ 0 ]) : 1 Determinant( lta[ 1 ]) : 1 registration took 10 minutes and 13 seconds. /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04 mri_convert /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/rawavg.mgz /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig.mgz --conform mri_convert /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/rawavg.mgz /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/rawavg.mgz... TR=15.00, TE=5.00, TI=-1.00, flip angle=30.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) Original Data has (1, 1, 1) mm size and (256, 256, 192) 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 /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig.mgz... mri_add_xform_to_header -c /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/transforms/talairach.xfm /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig.mgz /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Jul 26 14:50:47 CEST 2012 /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Jul 26 14:53:20 CEST 2012 /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5979, pval=0.2817 >= threshold=0.0050) awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/transforms/talairach_avi.log TalAviQA: 0.98153 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Thu Jul 26 14:53:20 CEST 2012 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri /opt/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Linux castor 2.6.34.10-0.6-default #1 SMP 2011-12-13 18:27:38 +0100 x86_64 x86_64 x86_64 GNU/Linux Thu Jul 26 14:53:20 CEST 2012 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.20897 /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20897/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20897/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=15.00, TE=5.00, TI=-1.00, flip angle=30.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.20897/nu0.mnc... -------------------------------------------------------- Iteration 1 Thu Jul 26 14:53:33 CEST 2012 nu_correct -clobber ./tmp.mri_nu_correct.mni.20897/nu0.mnc ./tmp.mri_nu_correct.mni.20897/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.20897/0/ [preisler@castor:/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/] [2012-07-26 14:53:33] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.20897/0/ ./tmp.mri_nu_correct.mni.20897/nu0.mnc ./tmp.mri_nu_correct.mni.20897/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 30 CV of field change: 0.000974415 [preisler@castor:/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/] [2012-07-26 14:54:22] running: /opt/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.20897/nu0.mnc ./tmp.mri_nu_correct.mni.20897/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Thu Jul 26 14:54:28 CEST 2012 nu_correct -clobber ./tmp.mri_nu_correct.mni.20897/nu1.mnc ./tmp.mri_nu_correct.mni.20897/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.20897/1/ [preisler@castor:/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/] [2012-07-26 14:54:28] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.20897/1/ ./tmp.mri_nu_correct.mni.20897/nu1.mnc ./tmp.mri_nu_correct.mni.20897/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 22 CV of field change: 0.000988107 [preisler@castor:/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/] [2012-07-26 14:55:06] running: /opt/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.20897/nu1.mnc ./tmp.mri_nu_correct.mni.20897/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.20897/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.20897/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.20897/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.20897/ones.mgz sysname Linux hostname castor machine x86_64 user preisler input ./tmp.mri_nu_correct.mni.20897/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.20897/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.20897/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.20897/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20897/input.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.20897/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.20897/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20897/input.mean.dat sysname Linux hostname castor machine x86_64 user preisler Loading ./tmp.mri_nu_correct.mni.20897/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 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.20897/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.20897/ones.mgz --i ./tmp.mri_nu_correct.mni.20897/nu2.mnc --sum ./tmp.mri_nu_correct.mni.20897/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20897/output.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.20897/ones.mgz --i ./tmp.mri_nu_correct.mni.20897/nu2.mnc --sum ./tmp.mri_nu_correct.mni.20897/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20897/output.mean.dat sysname Linux hostname castor machine x86_64 user preisler Loading ./tmp.mri_nu_correct.mni.20897/ones.mgz Loading ./tmp.mri_nu_correct.mni.20897/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.20897/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.20897/nu2.mnc ./tmp.mri_nu_correct.mni.20897/nu2.mnc mul 1.02360120410967868594 Saving result to './tmp.mri_nu_correct.mni.20897/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.20897/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.20897/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./tmp.mri_nu_correct.mni.20897/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 28 seconds. mapping (15, 123) to ( 3, 110) Thu Jul 26 14:57:53 CEST 2012 mri_nu_correct.mni done #-------------------------------------------- #@# Intensity Normalization Thu Jul 26 14:57:53 CEST 2012 /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.067 0.036 -0.049 -0.942; -0.031 1.023 -0.054 -18.659; 0.048 0.069 1.087 -15.780; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to T1.mgz 3D bias adjustment took 6 minutes and 55 seconds. MRIsplineNormalize(): npeaks = 14 Starting OpenSpline(): npoints = 14 white matter peak found at 111 white matter peak found at 104 gm peak at 77 (77), valley at 46 (46) csf peak at 39, setting threshold to 64 white matter peak found at 111 white matter peak found at 102 gm peak at 70 (70), valley at 57 (57) csf peak at 35, setting threshold to 58 #-------------------------------------------- #@# Skull Stripping Thu Jul 26 15:04:52 CEST 2012 /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Keeping brain edits brainmask.auto.mgz brainmask.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 mghRead(/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/brainmask.auto.mgz): could not read 65536 bytes at slice 76 ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Linux castor 2.6.34.10-0.6-default #1 SMP 2011-12-13 18:27:38 +0100 x86_64 x86_64 x86_64 GNU/Linux recon-all -s PTpost_P04 exited with ERRORS at Thu Jul 26 15:04:55 CEST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Thu Jul 26 18:37:31 CEST 2012 /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04 /opt/freesurfer/bin/recon-all -autorecon2 -s PTpost_P04 -no-isrunning subjid PTpost_P04 setenv SUBJECTS_DIR /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /srv/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux castor 2.6.34.10-0.6-default #1 SMP 2011-12-13 18:27:38 +0100 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse 13995420 kbytes vmemoryuse 53443920 kbytes descriptors 1024 memorylocked 64 kbytes maxproc 128526 total used free shared buffers cached Mem: 16465172 14371212 2093960 0 7876 10000112 -/+ buffers/cache: 4363224 12101948 Swap: 50339640 32788 50306852 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 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: 2012/07/26-16:37:31-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:32-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 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: 2012/07/26-16:37:32-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:32-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:32-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:32-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:33-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:34-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:34-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:34-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:34-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:34-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:34-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:34-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:34-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:34-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:35-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:35-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:35-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:35-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:35-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:35-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:35-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:35-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/07/26-16:37:36-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /opt/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #------------------------------------- #@# EM Registration Thu Jul 26 18:37:36 CEST 2012 /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri mri_em_register -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta aligning to atlas containing skull, setting unknown_nbr_spacing = 3 using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/opt/freesurfer/average/RB_all_2008-03-26.gca'... gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... mghRead(/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/brainmask.mgz, -1): read error mri_em_register: could not open mask volume brainmask.mgz. Linux castor 2.6.34.10-0.6-default #1 SMP 2011-12-13 18:27:38 +0100 x86_64 x86_64 x86_64 GNU/Linux recon-all -s PTpost_P04 exited with ERRORS at Thu Jul 26 18:37:44 CEST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Tue Jan 8 16:23:03 CET 2013 /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04 /opt/freesurfer/bin/recon-all -autorecon1 -s PTpost_P04/ subjid PTpost_P04 setenv SUBJECTS_DIR /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /srv/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux castor 2.6.34.10-0.6-default #1 SMP 2011-12-13 18:27:38 +0100 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse 13995420 kbytes vmemoryuse 53443920 kbytes descriptors 1024 memorylocked 64 kbytes maxproc 128526 total used free shared buffers cached Mem: 16465172 15670652 794520 0 267968 12206520 -/+ buffers/cache: 3196164 13269008 Swap: 50339640 158576 50181064 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 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: 2013/01/08-15:23:03-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 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: 2013/01/08-15:23:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:06-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:07-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:08-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:08-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:08-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:08-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-15:23:08-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /opt/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Tue Jan 8 16:23:08 CET 2013 Found 2 runs /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001.mgz /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04 mri_robust_template --mov /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001.mgz /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002.mgz --average 1 --template /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001-iscale.txt /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002-iscale.txt --subsample 200 --lta /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001.lta /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002.lta $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ --mov: Using /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001.mgz as movable/source volume. --mov: Using /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001.mgz'... reading source '/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002.mgz'... MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002.mgz ) to TP 1 ( /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001.mgz ) Registration::setSourceAndTarget ... Mov: (1, 1, 1)mm and dim (256, 256, 192) Dst: (1, 1, 1)mm and dim (256, 256, 192) Asserting both images: 1mm isotropic and (256, 256, 192) voxels - no Source reslice necessary - no Target reslice necessary Registration::findSaturation - Gaussian Pyramid - Gaussian Pyramid - Max Resolution used: 2 -- gpS ( 64 , 64 , 48 ) -- gpT ( 64 , 64 , 48 ) - computing centroids - computing initial transform -- using translation info - running loop to estimate saturation parameter: -- Iteration: 1 trying sat: 16 min sat: 0 ( -1 ), max sat: 16 ( 0.0889289 ), sat diff: 16 -- Iteration: 2 trying sat: 8 min sat: 8 ( 0.229024 ), max sat: 16 ( 0.0889289 ), sat diff: 8 -- Iteration: 3 trying sat: 12 min sat: 8 ( 0.229024 ), max sat: 12 ( 0.13274 ), sat diff: 4 -- Iteration: 4 trying sat: 10 min sat: 8 ( 0.229024 ), max sat: 10 ( 0.171133 ), sat diff: 2 -- Iteration: 5 trying sat: 9 min sat: 9 ( 0.197016 ), max sat: 10 ( 0.171133 ), sat diff: 1 -- Iteration: 6 trying sat: 9.5 - final SAT: 10 ( it: 6 , weight check 0.171133 <= 0.175 ) Registration::computeMultiresRegistration - computing centroids - computing initial transform -- using translation info - initial transform: Ti = [ ... 1.0000000000000 0 0 -0.4110469447285 0 1.0000000000000 0 0.1530539910717 0 0 1.0000000000000 0.3546136792791 0 0 0 1.0000000000000 ] - initial iscale: Ii =1 Resolution: 3 S( 32 32 24 ) T( 32 32 24 ) Iteration(f): 1 -- diff. to prev. transform: 0.450062 Iteration(f): 2 -- diff. to prev. transform: 0.0557345 Iteration(f): 3 -- diff. to prev. transform: 0.00654747 < 0.01 :-) Resolution: 2 S( 64 64 48 ) T( 64 64 48 ) Iteration(f): 1 -- diff. to prev. transform: 0.31352 Iteration(f): 2 -- diff. to prev. transform: 0.0484814 Iteration(f): 3 -- diff. to prev. transform: 0.0134828 Iteration(f): 4 -- diff. to prev. transform: 0.007309 < 0.01 :-) Resolution: 1 S( 128 128 96 ) T( 128 128 96 ) Iteration(f): 1 -- diff. to prev. transform: 0.416278 Iteration(f): 2 -- diff. to prev. transform: 0.0296166 Iteration(f): 3 -- diff. to prev. transform: 0.0265161 Iteration(f): 4 -- diff. to prev. transform: 0.00248624 < 0.01 :-) Resolution: 0 S( 256 256 192 ) T( 256 256 192 ) Iteration(f): 1 (subsample 200) -- diff. to prev. transform: 0.155631 Iteration(f): 2 (subsample 200) -- diff. to prev. transform: 0.00229369 < 0.01 :-) - final transform: Tf = [ ... 0.9999468775282 -0.0102213656869 0.0013288359668 0.7743403778683 0.0102309703053 0.9999200283784 -0.0074339824001 -0.7249879574123 -0.0012527442450 0.0074471827699 0.9999714846438 -0.6657203299900 0 0 0 1.0000000000000 ] - final iscale: If = 1.00501 warping movs and creating initial template... allow intensity scaling using median Writing final template: /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/rawavg.mgz Writing final transforms (warps etc.)... Determinant( lta[ 0 ]) : 1 Determinant( lta[ 1 ]) : 1 registration took 6 minutes and 43 seconds. /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04 mri_convert /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/rawavg.mgz /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig.mgz --conform mri_convert /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/rawavg.mgz /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/rawavg.mgz... TR=15.00, TE=5.00, TI=-1.00, flip angle=30.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) Original Data has (1, 1, 1) mm size and (256, 256, 192) 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 /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig.mgz... mri_add_xform_to_header -c /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/transforms/talairach.xfm /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig.mgz /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue Jan 8 16:30:22 CET 2013 /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue Jan 8 16:31:49 CET 2013 /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5979, pval=0.2817 >= threshold=0.0050) awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/transforms/talairach_avi.log TalAviQA: 0.98153 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Tue Jan 8 16:31:50 CET 2013 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri /opt/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Linux castor 2.6.34.10-0.6-default #1 SMP 2011-12-13 18:27:38 +0100 x86_64 x86_64 x86_64 GNU/Linux Tue Jan 8 16:31:50 CET 2013 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.20612 /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20612/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.20612/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=15.00, TE=5.00, TI=-1.00, flip angle=30.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.20612/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Jan 8 16:31:57 CET 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.20612/nu0.mnc ./tmp.mri_nu_correct.mni.20612/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.20612/0/ [preisler@castor:/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/] [2013-01-08 16:31:57] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.20612/0/ ./tmp.mri_nu_correct.mni.20612/nu0.mnc ./tmp.mri_nu_correct.mni.20612/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 30 CV of field change: 0.000974415 [preisler@castor:/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/] [2013-01-08 16:32:39] running: /opt/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.20612/nu0.mnc ./tmp.mri_nu_correct.mni.20612/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Tue Jan 8 16:32:45 CET 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.20612/nu1.mnc ./tmp.mri_nu_correct.mni.20612/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.20612/1/ [preisler@castor:/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/] [2013-01-08 16:32:45] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.20612/1/ ./tmp.mri_nu_correct.mni.20612/nu1.mnc ./tmp.mri_nu_correct.mni.20612/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 22 CV of field change: 0.000988107 [preisler@castor:/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/] [2013-01-08 16:33:17] running: /opt/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.20612/nu1.mnc ./tmp.mri_nu_correct.mni.20612/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.20612/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.20612/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.20612/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.20612/ones.mgz sysname Linux hostname castor machine x86_64 user preisler input ./tmp.mri_nu_correct.mni.20612/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.20612/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.20612/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.20612/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20612/input.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.20612/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.20612/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20612/input.mean.dat sysname Linux hostname castor machine x86_64 user preisler Loading ./tmp.mri_nu_correct.mni.20612/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 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.20612/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.20612/ones.mgz --i ./tmp.mri_nu_correct.mni.20612/nu2.mnc --sum ./tmp.mri_nu_correct.mni.20612/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20612/output.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.20612/ones.mgz --i ./tmp.mri_nu_correct.mni.20612/nu2.mnc --sum ./tmp.mri_nu_correct.mni.20612/sum.junk --avgwf ./tmp.mri_nu_correct.mni.20612/output.mean.dat sysname Linux hostname castor machine x86_64 user preisler Loading ./tmp.mri_nu_correct.mni.20612/ones.mgz Loading ./tmp.mri_nu_correct.mni.20612/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.20612/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.20612/nu2.mnc ./tmp.mri_nu_correct.mni.20612/nu2.mnc mul 1.02360120410967868594 Saving result to './tmp.mri_nu_correct.mni.20612/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.20612/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.20612/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./tmp.mri_nu_correct.mni.20612/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 19 seconds. mapping (15, 123) to ( 3, 110) Tue Jan 8 16:35:17 CET 2013 mri_nu_correct.mni done #-------------------------------------------- #@# Intensity Normalization Tue Jan 8 16:35:17 CET 2013 /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.067 0.036 -0.049 -0.942; -0.031 1.023 -0.054 -18.659; 0.048 0.069 1.087 -15.780; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to T1.mgz 3D bias adjustment took 4 minutes and 48 seconds. MRIsplineNormalize(): npeaks = 14 Starting OpenSpline(): npoints = 14 white matter peak found at 111 white matter peak found at 104 gm peak at 77 (77), valley at 46 (46) csf peak at 39, setting threshold to 64 white matter peak found at 111 white matter peak found at 102 gm peak at 70 (70), valley at 57 (57) csf peak at 35, setting threshold to 58 #-------------------------------------------- #@# Skull Stripping Tue Jan 8 16:40:08 CET 2013 /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Keeping brain edits brainmask.auto.mgz brainmask.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 mghRead(/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/brainmask.auto.mgz): could not read 65536 bytes at slice 76 ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Linux castor 2.6.34.10-0.6-default #1 SMP 2011-12-13 18:27:38 +0100 x86_64 x86_64 x86_64 GNU/Linux recon-all -s PTpost_P04 exited with ERRORS at Tue Jan 8 16:40:10 CET 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Tue Jan 8 18:09:00 CET 2013 /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04 /opt/freesurfer/bin/recon-all -autorecon1 -s PTpost_P04 subjid PTpost_P04 setenv SUBJECTS_DIR /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer FREESURFER_HOME /opt/freesurfer Actual FREESURFER_HOME /srv/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux castor 2.6.34.10-0.6-default #1 SMP 2011-12-13 18:27:38 +0100 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse 13995420 kbytes vmemoryuse 53443920 kbytes descriptors 1024 memorylocked 64 kbytes maxproc 128526 total used free shared buffers cached Mem: 16465172 14125308 2339864 0 265068 11289540 -/+ buffers/cache: 2570700 13894472 Swap: 50339640 158596 50181044 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 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: 2013/01/08-17:09:00-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 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: 2013/01/08-17:09:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:01-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:02-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:03-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:03-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:03-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:03-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:03-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:03-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:03-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:03-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:04-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/08-17:09:05-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: preisler Machine: castor Platform: Linux PlatformVersion: 2.6.34.10-0.6-default CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /opt/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /opt/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Tue Jan 8 18:09:05 CET 2013 Found 2 runs /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001.mgz /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04 mri_robust_template --mov /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001.mgz /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002.mgz --average 1 --template /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001-iscale.txt /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002-iscale.txt --subsample 200 --lta /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001.lta /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002.lta $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ --mov: Using /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001.mgz as movable/source volume. --mov: Using /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001.mgz'... reading source '/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002.mgz'... MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/002.mgz ) to TP 1 ( /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig/001.mgz ) Registration::setSourceAndTarget ... Mov: (1, 1, 1)mm and dim (256, 256, 192) Dst: (1, 1, 1)mm and dim (256, 256, 192) Asserting both images: 1mm isotropic and (256, 256, 192) voxels - no Source reslice necessary - no Target reslice necessary Registration::findSaturation - Gaussian Pyramid - Gaussian Pyramid - Max Resolution used: 2 -- gpS ( 64 , 64 , 48 ) -- gpT ( 64 , 64 , 48 ) - computing centroids - computing initial transform -- using translation info - running loop to estimate saturation parameter: -- Iteration: 1 trying sat: 16 min sat: 0 ( -1 ), max sat: 16 ( 0.0889289 ), sat diff: 16 -- Iteration: 2 trying sat: 8 min sat: 8 ( 0.229024 ), max sat: 16 ( 0.0889289 ), sat diff: 8 -- Iteration: 3 trying sat: 12 min sat: 8 ( 0.229024 ), max sat: 12 ( 0.13274 ), sat diff: 4 -- Iteration: 4 trying sat: 10 min sat: 8 ( 0.229024 ), max sat: 10 ( 0.171133 ), sat diff: 2 -- Iteration: 5 trying sat: 9 min sat: 9 ( 0.197016 ), max sat: 10 ( 0.171133 ), sat diff: 1 -- Iteration: 6 trying sat: 9.5 - final SAT: 10 ( it: 6 , weight check 0.171133 <= 0.175 ) Registration::computeMultiresRegistration - computing centroids - computing initial transform -- using translation info - initial transform: Ti = [ ... 1.0000000000000 0 0 -0.4110469447285 0 1.0000000000000 0 0.1530539910717 0 0 1.0000000000000 0.3546136792791 0 0 0 1.0000000000000 ] - initial iscale: Ii =1 Resolution: 3 S( 32 32 24 ) T( 32 32 24 ) Iteration(f): 1 -- diff. to prev. transform: 0.450062 Iteration(f): 2 -- diff. to prev. transform: 0.0557345 Iteration(f): 3 -- diff. to prev. transform: 0.00654747 < 0.01 :-) Resolution: 2 S( 64 64 48 ) T( 64 64 48 ) Iteration(f): 1 -- diff. to prev. transform: 0.31352 Iteration(f): 2 -- diff. to prev. transform: 0.0484814 Iteration(f): 3 -- diff. to prev. transform: 0.0134828 Iteration(f): 4 -- diff. to prev. transform: 0.007309 < 0.01 :-) Resolution: 1 S( 128 128 96 ) T( 128 128 96 ) Iteration(f): 1 -- diff. to prev. transform: 0.416278 Iteration(f): 2 -- diff. to prev. transform: 0.0296166 Iteration(f): 3 -- diff. to prev. transform: 0.0265161 Iteration(f): 4 -- diff. to prev. transform: 0.00248624 < 0.01 :-) Resolution: 0 S( 256 256 192 ) T( 256 256 192 ) Iteration(f): 1 (subsample 200) -- diff. to prev. transform: 0.155631 Iteration(f): 2 (subsample 200) -- diff. to prev. transform: 0.00229369 < 0.01 :-) - final transform: Tf = [ ... 0.9999468775282 -0.0102213656869 0.0013288359668 0.7743403778683 0.0102309703053 0.9999200283784 -0.0074339824001 -0.7249879574123 -0.0012527442450 0.0074471827699 0.9999714846438 -0.6657203299900 0 0 0 1.0000000000000 ] - final iscale: If = 1.00501 warping movs and creating initial template... allow intensity scaling using median Writing final template: /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/rawavg.mgz Writing final transforms (warps etc.)... Determinant( lta[ 0 ]) : 1 Determinant( lta[ 1 ]) : 1 registration took 6 minutes and 39 seconds. /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04 mri_convert /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/rawavg.mgz /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig.mgz --conform mri_convert /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/rawavg.mgz /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/rawavg.mgz... TR=15.00, TE=5.00, TI=-1.00, flip angle=30.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) Original Data has (1, 1, 1) mm size and (256, 256, 192) 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 /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig.mgz... mri_add_xform_to_header -c /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/transforms/talairach.xfm /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig.mgz /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue Jan 8 18:16:12 CET 2013 /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue Jan 8 18:17:46 CET 2013 /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5979, pval=0.2817 >= threshold=0.0050) awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/transforms/talairach_avi.log TalAviQA: 0.98153 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Tue Jan 8 18:17:46 CET 2013 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri /opt/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Linux castor 2.6.34.10-0.6-default #1 SMP 2011-12-13 18:27:38 +0100 x86_64 x86_64 x86_64 GNU/Linux Tue Jan 8 18:17:46 CET 2013 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.23666 /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.23666/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.23666/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=15.00, TE=5.00, TI=-1.00, flip angle=30.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.23666/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Jan 8 18:17:53 CET 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.23666/nu0.mnc ./tmp.mri_nu_correct.mni.23666/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.23666/0/ [preisler@castor:/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/] [2013-01-08 18:17:53] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.23666/0/ ./tmp.mri_nu_correct.mni.23666/nu0.mnc ./tmp.mri_nu_correct.mni.23666/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 30 CV of field change: 0.000974415 [preisler@castor:/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/] [2013-01-08 18:18:36] running: /opt/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.23666/nu0.mnc ./tmp.mri_nu_correct.mni.23666/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Tue Jan 8 18:18:41 CET 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.23666/nu1.mnc ./tmp.mri_nu_correct.mni.23666/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.23666/1/ [preisler@castor:/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/] [2013-01-08 18:18:41] running: /opt/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.23666/1/ ./tmp.mri_nu_correct.mni.23666/nu1.mnc ./tmp.mri_nu_correct.mni.23666/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 22 CV of field change: 0.000988107 [preisler@castor:/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/] [2013-01-08 18:19:15] running: /opt/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.23666/nu1.mnc ./tmp.mri_nu_correct.mni.23666/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.23666/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.23666/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.23666/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.23666/ones.mgz sysname Linux hostname castor machine x86_64 user preisler input ./tmp.mri_nu_correct.mni.23666/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.23666/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.23666/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.23666/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23666/input.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.23666/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.23666/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23666/input.mean.dat sysname Linux hostname castor machine x86_64 user preisler Loading ./tmp.mri_nu_correct.mni.23666/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 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.23666/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.23666/ones.mgz --i ./tmp.mri_nu_correct.mni.23666/nu2.mnc --sum ./tmp.mri_nu_correct.mni.23666/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23666/output.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.23666/ones.mgz --i ./tmp.mri_nu_correct.mni.23666/nu2.mnc --sum ./tmp.mri_nu_correct.mni.23666/sum.junk --avgwf ./tmp.mri_nu_correct.mni.23666/output.mean.dat sysname Linux hostname castor machine x86_64 user preisler Loading ./tmp.mri_nu_correct.mni.23666/ones.mgz Loading ./tmp.mri_nu_correct.mni.23666/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.23666/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.23666/nu2.mnc ./tmp.mri_nu_correct.mni.23666/nu2.mnc mul 1.02360120410967868594 Saving result to './tmp.mri_nu_correct.mni.23666/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.23666/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.23666/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./tmp.mri_nu_correct.mni.23666/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 20 seconds. mapping (15, 123) to ( 3, 110) Tue Jan 8 18:21:20 CET 2013 mri_nu_correct.mni done #-------------------------------------------- #@# Intensity Normalization Tue Jan 8 18:21:20 CET 2013 /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.067 0.036 -0.049 -0.942; -0.031 1.023 -0.054 -18.659; 0.048 0.069 1.087 -15.780; 0.000 0.000 0.000 1.000; INFO: Modifying talairach volume c_(r,a,s) based on average_305 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to T1.mgz 3D bias adjustment took 4 minutes and 43 seconds. MRIsplineNormalize(): npeaks = 14 Starting OpenSpline(): npoints = 14 white matter peak found at 111 white matter peak found at 104 gm peak at 77 (77), valley at 46 (46) csf peak at 39, setting threshold to 64 white matter peak found at 111 white matter peak found at 102 gm peak at 70 (70), valley at 57 (57) csf peak at 35, setting threshold to 58 #-------------------------------------------- #@# Skull Stripping Tue Jan 8 18:26:05 CET 2013 /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Keeping brain edits brainmask.auto.mgz brainmask.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 mghRead(/mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri/brainmask.auto.mgz): could not read 65536 bytes at slice 76 ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Linux castor 2.6.34.10-0.6-default #1 SMP 2011-12-13 18:27:38 +0100 x86_64 x86_64 x86_64 GNU/Linux recon-all -s PTpost_P04 exited with ERRORS at Tue Jan 8 18:26:07 CET 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting