Mon Oct 17 11:47:46 CEST 2016 /scr/eber2/intstats/freesurfer/is09 /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64/bin/recon-all -i /scr/eber2/intstats/freesurfer/unpacked_dicom/19417.87_131117_180626_S10_t1_mpr_sag_ADNI_32Ch/00100001 -subjid is09 subjid is09 setenv SUBJECTS_DIR /scr/eber2/intstats/freesurfer FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64 Actual FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-precise-amd64 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux brombeere 4.4.0-38-generic #57-Ubuntu SMP Tue Sep 6 15:42:33 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 15642 maxlocks unlimited maxsignal 15642 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 4045300 907688 837644 43520 2299968 2776872 Swap: 48827388 0 48827388 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:47:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/10/17-09:47:51-GMT BuildTimeStamp: Oct 29 2013 21:04:33 CVS: $Id: mri_segstats.c,v 1.101 2013/08/20 15:52:54 greve Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /scr/eber2/intstats/freesurfer/is09 mri_convert /scr/eber2/intstats/freesurfer/unpacked_dicom/19417.87_131117_180626_S10_t1_mpr_sag_ADNI_32Ch/00100001 /scr/eber2/intstats/freesurfer/is09/mri/orig/001.mgz mri_convert /scr/eber2/intstats/freesurfer/unpacked_dicom/19417.87_131117_180626_S10_t1_mpr_sag_ADNI_32Ch/00100001 /scr/eber2/intstats/freesurfer/is09/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /scr/eber2/intstats/freesurfer/unpacked_dicom/19417.87_131117_180626_S10_t1_mpr_sag_ADNI_32Ch/00100001... Getting Series No INFO: Found 178 files in /scr/eber2/intstats/freesurfer/unpacked_dicom/19417.87_131117_180626_S10_t1_mpr_sag_ADNI_32Ch INFO: Scanning for Series Number 10 Scanning Directory INFO: found 176 files in series INFO: loading series header info. RunNo = 9 INFO: sorting. INFO: (240 256 176), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /scr/eber2/intstats/freesurfer/unpacked_dicom/19417.87_131117_180626_S10_t1_mpr_sag_ADNI_32Ch/00100001 Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName 19417.87 Date and time StudyDate 20131117 StudyTime 180626.875000 SeriesTime 185924.953000 AcqTime 185002.897500 Acquisition parameters PulseSeq *tfl3d1_ns Protocol t1_mpr_sag_ADNI_32Ch PhEncDir ROW EchoNo 1 FlipAngle 9 EchoTime 2.96 InversionTime 900 RepetitionTime 2300 PhEncFOV 240 ReadoutFOV 256 Image information RunNo 9 SeriesNo 10 ImageNo 1 NImageRows 256 NImageCols 240 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 87.5000 120.0000 128.0000 VolRes 1.0000 1.0000 1.0000 VolDim 240 256 176 Vc -0.0000 -1.0000 0.0000 Vr -0.0000 -0.0000 -1.0000 Vs -1.0000 -0.0000 0.0000 VolCenter -0.5000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) INFO: no Siemens slice order reversal detected (good!). TR=2300.00, TE=2.96, TI=900.00, flip angle=9.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) writing to /scr/eber2/intstats/freesurfer/is09/mri/orig/001.mgz... #------------------------------------------ Started at Mon Oct 17 11:47:45 CEST 2016 Ended at Mon Oct 17 11:48:23 CEST 2016 #@#%# recon-all-run-time-hours 0.011 recon-all -s is09 finished without error at Mon Oct 17 11:48:24 CEST 2016 New invocation of recon-all Mon Oct 17 11:49:34 CEST 2016 /scr/eber2/intstats/freesurfer/is09 /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64/bin/recon-all -autorecon1 -nuintensitycor-3T -subjid is09 subjid is09 setenv SUBJECTS_DIR /scr/eber2/intstats/freesurfer FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64 Actual FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-precise-amd64 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux brombeere 4.4.0-38-generic #57-Ubuntu SMP Tue Sep 6 15:42:33 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 15642 maxlocks unlimited maxsignal 15642 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 4045300 949984 757716 43520 2337600 2733992 Swap: 48827388 0 48827388 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-09:49:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/10/17-09:49:39-GMT BuildTimeStamp: Oct 29 2013 21:04:33 CVS: $Id: mri_segstats.c,v 1.101 2013/08/20 15:52:54 greve Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Mon Oct 17 11:49:40 CEST 2016 Found 1 runs /scr/eber2/intstats/freesurfer/is09/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /scr/eber2/intstats/freesurfer/is09/mri/orig/001.mgz /scr/eber2/intstats/freesurfer/is09/mri/rawavg.mgz /scr/eber2/intstats/freesurfer/is09 mri_convert /scr/eber2/intstats/freesurfer/is09/mri/rawavg.mgz /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz --conform mri_convert /scr/eber2/intstats/freesurfer/is09/mri/rawavg.mgz /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /scr/eber2/intstats/freesurfer/is09/mri/rawavg.mgz... TR=2300.00, TE=2.96, TI=900.00, flip angle=9.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) Original Data has (1, 1, 1) mm size and (240, 256, 176) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz... mri_add_xform_to_header -c /scr/eber2/intstats/freesurfer/is09/mri/transforms/talairach.xfm /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Oct 17 11:49:54 CEST 2016 /scr/eber2/intstats/freesurfer/is09/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux brombeere 4.4.0-38-generic #57-Ubuntu SMP Tue Sep 6 15:42:33 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s is09 exited with ERRORS at Mon Oct 17 11:50:01 CEST 2016 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Mon Oct 17 12:00:38 CEST 2016 /scr/eber2/intstats/freesurfer/is09 /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64/bin/recon-all -autorecon1 -nuintensitycor-3T -subjid is09 subjid is09 setenv SUBJECTS_DIR /scr/eber2/intstats/freesurfer FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64 Actual FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-precise-amd64 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux brombeere 4.4.0-38-generic #57-Ubuntu SMP Tue Sep 6 15:42:33 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 15642 maxlocks unlimited maxsignal 15642 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 4045300 973004 647876 46516 2424420 2707828 Swap: 48827388 0 48827388 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:00:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/10/17-10:00:43-GMT BuildTimeStamp: Oct 29 2013 21:04:33 CVS: $Id: mri_segstats.c,v 1.101 2013/08/20 15:52:54 greve Exp $ User: wolff Machine: brombeere Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Mon Oct 17 12:00:44 CEST 2016 Found 1 runs /scr/eber2/intstats/freesurfer/is09/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /scr/eber2/intstats/freesurfer/is09/mri/orig/001.mgz /scr/eber2/intstats/freesurfer/is09/mri/rawavg.mgz /scr/eber2/intstats/freesurfer/is09 mri_convert /scr/eber2/intstats/freesurfer/is09/mri/rawavg.mgz /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz --conform mri_convert /scr/eber2/intstats/freesurfer/is09/mri/rawavg.mgz /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /scr/eber2/intstats/freesurfer/is09/mri/rawavg.mgz... TR=2300.00, TE=2.96, TI=900.00, flip angle=9.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) Original Data has (1, 1, 1) mm size and (240, 256, 176) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz... mri_add_xform_to_header -c /scr/eber2/intstats/freesurfer/is09/mri/transforms/talairach.xfm /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Oct 17 12:00:58 CEST 2016 /scr/eber2/intstats/freesurfer/is09/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux brombeere 4.4.0-38-generic #57-Ubuntu SMP Tue Sep 6 15:42:33 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s is09 exited with ERRORS at Mon Oct 17 12:01:04 CEST 2016 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Mon Oct 17 12:16:45 CEST 2016 /scr/eber2/intstats/freesurfer/is09 /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/bin/recon-all -autorecon1 -nuintensitycor-3T -subjid is09 subjid is09 setenv SUBJECTS_DIR /scr/eber2/intstats/freesurfer FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64 Actual FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-precise-amd64 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux eber 4.4.0-40-generic #60~14.04.1-Ubuntu SMP Fri Sep 23 20:37:40 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 257240 maxlocks unlimited maxsignal 257240 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 65956556 64553516 1403040 5628 953940 61391536 -/+ buffers/cache: 2208040 63748516 Swap: 48827388 0 48827388 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:48-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:16:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/10/17-10:16:50-GMT BuildTimeStamp: Oct 29 2013 21:04:33 CVS: $Id: mri_segstats.c,v 1.101 2013/08/20 15:52:54 greve Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64 Previous: /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64 #-------------------------------------------- #@# MotionCor Mon Oct 17 12:16:51 CEST 2016 Found 1 runs /scr/eber2/intstats/freesurfer/is09/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /scr/eber2/intstats/freesurfer/is09/mri/orig/001.mgz /scr/eber2/intstats/freesurfer/is09/mri/rawavg.mgz /scr/eber2/intstats/freesurfer/is09 mri_convert /scr/eber2/intstats/freesurfer/is09/mri/rawavg.mgz /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz --conform mri_convert /scr/eber2/intstats/freesurfer/is09/mri/rawavg.mgz /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /scr/eber2/intstats/freesurfer/is09/mri/rawavg.mgz... TR=2300.00, TE=2.96, TI=900.00, flip angle=9.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) Original Data has (1, 1, 1) mm size and (240, 256, 176) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz... mri_add_xform_to_header -c /scr/eber2/intstats/freesurfer/is09/mri/transforms/talairach.xfm /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Oct 17 12:17:05 CEST 2016 /scr/eber2/intstats/freesurfer/is09/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz New invocation of recon-all Mon Oct 17 12:17:42 CEST 2016 /scr/eber2/intstats/freesurfer/is09 /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64/bin/recon-all -autorecon1 -nuintensitycor-3T -subjid is09 subjid is09 setenv SUBJECTS_DIR /scr/eber2/intstats/freesurfer FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64 Actual FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-precise-amd64 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux ren 4.4.0-38-generic #57-Ubuntu SMP Tue Sep 6 15:42:33 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 31775 maxlocks unlimited maxsignal 31775 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 8174060 1427216 4624424 162544 2122420 6249996 Swap: 48829532 0 48829532 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:17:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:17:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:17:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:17:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:17:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:17:56-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:17:58-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:00-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:02-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:04-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:06-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:12-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:19-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:21-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:24-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:26-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:28-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:30-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:32-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:47-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:18:57-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:19:05-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-10:19:08-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/10/17-10:19:12-GMT BuildTimeStamp: Oct 29 2013 21:04:33 CVS: $Id: mri_segstats.c,v 1.101 2013/08/20 15:52:54 greve Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Oct 17 12:20:02 CEST 2016 /scr/eber2/intstats/freesurfer/is09/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7744, pval=0.6675 >= threshold=0.0050) awk -f /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/bin/extract_talairach_avi_QA.awk /scr/eber2/intstats/freesurfer/is09/mri/transforms/talairach_avi.log tal_QC_AZS /scr/eber2/intstats/freesurfer/is09/mri/transforms/talairach_avi.log TalAviQA: 0.96909 z-score: -2 #-------------------------------------------- #@# Nu Intensity Correction Mon Oct 17 12:20:02 CEST 2016 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 /scr/eber2/intstats/freesurfer/is09/mri /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 nIters 1 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux eber 4.4.0-40-generic #60~14.04.1-Ubuntu SMP Fri Sep 23 20:37:40 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Mon Oct 17 12:20:02 CEST 2016 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.4170 /scr/eber2/intstats/freesurfer/is09/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4170/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.4170/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=2300.00, TE=2.96, TI=900.00, flip angle=9.00 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.4170/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Oct 17 12:20:05 CEST 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.4170/nu0.mnc ./tmp.mri_nu_correct.mni.4170/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.4170/0/ -iterations 1000 -distance 50 defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [wolff@eber:/scr/eber2/intstats/freesurfer/is09/mri/] [2016-10-17 12:20:05] running: /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.4170/0/ ./tmp.mri_nu_correct.mni.4170/nu0.mnc ./tmp.mri_nu_correct.mni.4170/nu1.imp Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 62 CV of field change: 0.000979967 [wolff@eber:/scr/eber2/intstats/freesurfer/is09/mri/] [2016-10-17 12:21:38] running: /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.4170/nu0.mnc ./tmp.mri_nu_correct.mni.4170/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.4170/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.4170/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /scr/eber2/intstats/freesurfer/is09/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.4170/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.4170/ones.mgz sysname Linux hostname eber machine x86_64 user wolff input ./tmp.mri_nu_correct.mni.4170/nu1.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.4170/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.4170/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.4170/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4170/input.mean.dat $Id: mri_segstats.c,v 1.101 2013/08/20 15:52:54 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4170/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.4170/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4170/input.mean.dat sysname Linux hostname eber machine x86_64 user wolff UseRobust 0 Loading ./tmp.mri_nu_correct.mni.4170/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.4170/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4170/ones.mgz --i ./tmp.mri_nu_correct.mni.4170/nu1.mnc --sum ./tmp.mri_nu_correct.mni.4170/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4170/output.mean.dat $Id: mri_segstats.c,v 1.101 2013/08/20 15:52:54 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.4170/ones.mgz --i ./tmp.mri_nu_correct.mni.4170/nu1.mnc --sum ./tmp.mri_nu_correct.mni.4170/sum.junk --avgwf ./tmp.mri_nu_correct.mni.4170/output.mean.dat sysname Linux hostname eber machine x86_64 user wolff UseRobust 0 Loading ./tmp.mri_nu_correct.mni.4170/ones.mgz Loading ./tmp.mri_nu_correct.mni.4170/nu1.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.4170/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.4170/nu1.mnc ./tmp.mri_nu_correct.mni.4170/nu1.mnc mul .91727736055098766296 Saving result to './tmp.mri_nu_correct.mni.4170/nu1.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.4170/nu1.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.4170/nu1.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.4170/nu1.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 12 seconds. mapping ( 9, 165) to ( 3, 110) Mon Oct 17 12:22:36 CEST 2016 mri_nu_correct.mni done mri_add_xform_to_header -c /scr/eber2/intstats/freesurfer/is09/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Mon Oct 17 12:22:38 CEST 2016 /scr/eber2/intstats/freesurfer/is09/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.121 0.052 0.001 -0.790; -0.041 1.186 0.177 -24.730; 0.002 -0.325 1.191 -3.403; 0.000 0.000 0.000 1.000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 16 Starting OpenSpline(): npoints = 16 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 69 (69), valley at 45 (45) csf peak at 33, setting threshold to 57 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 69 (69), valley at 57 (57) csf peak at 29, setting threshold to 55 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 3 minutes and 17 seconds. #-------------------------------------------- #@# Skull Stripping Mon Oct 17 12:25:56 CEST 2016 /scr/eber2/intstats/freesurfer/is09/mri mri_em_register -skull nu.mgz /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/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=8.0 skull bounding box = (47, 42, 34) --> (209, 255, 237) using (101, 113, 136) as brain centroid... mean wm in atlas = 126, using box (81,87,111) --> (120, 139,161) to find MRI wm before smoothing, mri peak at 108 after smoothing, mri peak at 108, scaling input intensities by 1.167 scaling channel 0 by 1.16667 initial log_p = -4.7 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.514502 @ (-9.091, -9.091, -27.273) max log p = -4.409693 @ (4.545, 4.545, 4.545) max log p = -4.359390 @ (2.273, -2.273, -2.273) max log p = -4.338389 @ (3.409, 1.136, 1.136) max log p = -4.334817 @ (-1.705, -1.705, -1.705) max log p = -4.309035 @ (0.284, 0.284, 0.284) Found translation: (-0.3, -7.1, -25.3): log p = -4.309 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.3 (thresh=-4.3) 1.150 0.000 0.000 -19.191; 0.000 1.135 0.169 -39.118; 0.000 -0.112 0.997 -10.516; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.150 0.000 0.000 -19.191; 0.000 1.220 0.182 -51.136; 0.000 -0.112 0.997 -10.516; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.1, old_max_log_p =-4.1 (thresh=-4.1) 1.150 0.000 0.000 -19.191; 0.000 1.220 0.182 -51.136; 0.000 -0.112 0.997 -10.516; 0.000 0.000 0.000 1.000; reducing scale to 0.2500 **************************************** Nine parameter search. iteration 3 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.1 (thresh=-4.1) 1.083 -0.034 -0.068 0.165; 0.036 1.266 0.186 -59.941; 0.078 -0.116 1.032 -24.463; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.0, old_max_log_p =-4.0 (thresh=-4.0) 1.083 -0.034 -0.068 0.165; 0.036 1.266 0.186 -59.941; 0.078 -0.116 1.032 -24.463; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-4.0 (thresh=-4.0) 1.084 -0.065 -0.063 2.806; 0.061 1.265 0.168 -60.147; 0.069 -0.095 1.035 -26.326; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 6 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-3.9, old_max_log_p =-3.9 (thresh=-3.9) 1.086 -0.066 -0.063 2.518; 0.061 1.262 0.168 -59.722; 0.070 -0.095 1.038 -26.636; 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 1.08649 -0.06551 -0.06315 2.51782; 0.06097 1.26158 0.16755 -59.72240; 0.06962 -0.09488 1.03752 -26.63585; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.08649 -0.06551 -0.06315 2.51782; 0.06097 1.26158 0.16755 -59.72240; 0.06962 -0.09488 1.03752 -26.63585; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 009: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.086 -0.066 -0.063 2.518; 0.061 1.262 0.168 -59.722; 0.070 -0.095 1.038 -26.636; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -3.9 (old=-4.7) transform before final EM align: 1.086 -0.066 -0.063 2.518; 0.061 1.262 0.168 -59.722; 0.070 -0.095 1.038 -26.636; 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 1.08649 -0.06551 -0.06315 2.51782; 0.06097 1.26158 0.16755 -59.72240; 0.06962 -0.09488 1.03752 -26.63585; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.08649 -0.06551 -0.06315 2.51782; 0.06097 1.26158 0.16755 -59.72240; 0.06962 -0.09488 1.03752 -26.63585; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 011: -log(p) = 4.4 tol 0.000000 final transform: 1.086 -0.066 -0.063 2.518; 0.061 1.262 0.168 -59.722; 0.070 -0.095 1.038 -26.636; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 39 minutes and 31 seconds. mri_watershed -T1 -brain_atlas /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/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=128 y=110 z=134 r=89 first estimation of the main basin volume: 3020623 voxels Looking for seedpoints 2 found in the cerebellum 15 found in the rest of the brain global maximum in x=155, y=108, z=100, Imax=255 CSF=13, 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=19387469695 voxels, voxel volume =1.000 = 19387469695 mmm3 = 19387469.824 cm3 done. PostAnalyze...Basin Prior 102 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=126,y=118, z=128, r=9669 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=16 , nb = 45297 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=22 , nb = -1034493137 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=8 , nb = 1078098870 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=17 , nb = 1063481312 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=15 , nb = 1081076010 OTHER CSF_MIN=0, CSF_intensity=13, CSF_MAX=21 , nb = -1093558746 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 16, 30, 49, 67 after analyzing : 16, 42, 49, 48 RIGHT_CER before analyzing : 22, 34, 52, 79 after analyzing : 22, 46, 52, 54 LEFT_CER before analyzing : 8, 15, 48, 74 after analyzing : 8, 37, 48, 46 RIGHT_BRAIN before analyzing : 17, 30, 48, 67 after analyzing : 17, 42, 48, 48 LEFT_BRAIN before analyzing : 15, 29, 49, 66 after analyzing : 15, 42, 49, 48 OTHER before analyzing : 21, 40, 72, 85 after analyzing : 21, 61, 72, 67 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...73 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.012 curvature mean = 67.089, std = 7.614 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 1.79, sigma = 3.19 after rotation: sse = 1.79, sigma = 3.19 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 1.90, its var is 2.97 before Erosion-Dilatation 0.23% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...43 iterations mri_strip_skull: done peeling brain Brain Size = 1497672 voxels, voxel volume = 1.000 mm3 = 1497672 mmm3 = 1497.672 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------------ Started at Mon Oct 17 12:16:45 CEST 2016 Ended at Mon Oct 17 13:06:01 CEST 2016 #@#%# recon-all-run-time-hours 0.821 recon-all -s is09 finished without error at Mon Oct 17 13:06:01 CEST 2016 New invocation of recon-all Mon Oct 17 13:19:39 CEST 2016 /scr/eber2/intstats/freesurfer/is09 /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64/bin/recon-all -autorecon1 -nuintensitycor-3T -subjid is09 subjid is09 setenv SUBJECTS_DIR /scr/eber2/intstats/freesurfer FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64 Actual FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-precise-amd64 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux ren 4.4.0-38-generic #57-Ubuntu SMP Tue Sep 6 15:42:33 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 31775 maxlocks unlimited maxsignal 31775 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 8174060 1422568 4325584 162564 2425908 6254328 Swap: 48829532 0 48829532 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:41-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:43-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:44-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:45-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:19:46-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/10/17-11:19:46-GMT BuildTimeStamp: Oct 29 2013 21:04:33 CVS: $Id: mri_segstats.c,v 1.101 2013/08/20 15:52:54 greve Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Mon Oct 17 13:19:47 CEST 2016 Found 1 runs /scr/eber2/intstats/freesurfer/is09/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /scr/eber2/intstats/freesurfer/is09/mri/orig/001.mgz /scr/eber2/intstats/freesurfer/is09/mri/rawavg.mgz /scr/eber2/intstats/freesurfer/is09 mri_convert /scr/eber2/intstats/freesurfer/is09/mri/rawavg.mgz /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz --conform mri_convert /scr/eber2/intstats/freesurfer/is09/mri/rawavg.mgz /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /scr/eber2/intstats/freesurfer/is09/mri/rawavg.mgz... TR=2300.00, TE=2.96, TI=900.00, flip angle=9.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) Original Data has (1, 1, 1) mm size and (240, 256, 176) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz... mri_add_xform_to_header -c /scr/eber2/intstats/freesurfer/is09/mri/transforms/talairach.xfm /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Oct 17 13:20:08 CEST 2016 /scr/eber2/intstats/freesurfer/is09/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux ren 4.4.0-38-generic #57-Ubuntu SMP Tue Sep 6 15:42:33 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s is09 exited with ERRORS at Mon Oct 17 13:20:16 CEST 2016 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Mon Oct 17 13:58:13 CEST 2016 /scr/eber2/intstats/freesurfer/is09 /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/bin/recon-all -autorecon1 -nuintensitycor-3T -subjid is09 subjid is09 setenv SUBJECTS_DIR /scr/eber2/intstats/freesurfer FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64 Actual FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-precise-amd64 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux eber 4.4.0-40-generic #60~14.04.1-Ubuntu SMP Fri Sep 23 20:37:40 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 257240 maxlocks unlimited maxsignal 257240 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 65956556 63869688 2086868 5628 956272 60694320 -/+ buffers/cache: 2219096 63737460 Swap: 48827388 0 48827388 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:13-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:14-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:15-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:16-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-11:58:17-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/10/17-11:58:17-GMT BuildTimeStamp: Oct 29 2013 21:04:33 CVS: $Id: mri_segstats.c,v 1.101 2013/08/20 15:52:54 greve Exp $ User: wolff Machine: eber Platform: Linux PlatformVersion: 4.4.0-40-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64 Previous: /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64 #-------------------------------------------- #@# MotionCor Mon Oct 17 13:58:18 CEST 2016 Found 1 runs /scr/eber2/intstats/freesurfer/is09/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /scr/eber2/intstats/freesurfer/is09/mri/orig/001.mgz /scr/eber2/intstats/freesurfer/is09/mri/rawavg.mgz /scr/eber2/intstats/freesurfer/is09 mri_convert /scr/eber2/intstats/freesurfer/is09/mri/rawavg.mgz /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz --conform mri_convert /scr/eber2/intstats/freesurfer/is09/mri/rawavg.mgz /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /scr/eber2/intstats/freesurfer/is09/mri/rawavg.mgz... TR=2300.00, TE=2.96, TI=900.00, flip angle=9.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) Original Data has (1, 1, 1) mm size and (240, 256, 176) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz... mri_add_xform_to_header -c /scr/eber2/intstats/freesurfer/is09/mri/transforms/talairach.xfm /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Oct 17 13:58:31 CEST 2016 /scr/eber2/intstats/freesurfer/is09/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm 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 Mon Oct 17 14:01:37 CEST 2016 /scr/eber2/intstats/freesurfer/is09/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7906, pval=0.8469 >= threshold=0.0050) awk -f /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/bin/extract_talairach_avi_QA.awk /scr/eber2/intstats/freesurfer/is09/mri/transforms/talairach_avi.log tal_QC_AZS /scr/eber2/intstats/freesurfer/is09/mri/transforms/talairach_avi.log TalAviQA: 0.96909 z-score: -2 #-------------------------------------------- #@# Nu Intensity Correction Mon Oct 17 14:01:38 CEST 2016 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 /scr/eber2/intstats/freesurfer/is09/mri /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 nIters 1 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux eber 4.4.0-40-generic #60~14.04.1-Ubuntu SMP Fri Sep 23 20:37:40 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux Mon Oct 17 14:01:38 CEST 2016 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.8803 /scr/eber2/intstats/freesurfer/is09/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.8803/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.8803/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=2300.00, TE=2.96, TI=900.00, flip angle=9.00 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.8803/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Oct 17 14:01:41 CEST 2016 nu_correct -clobber ./tmp.mri_nu_correct.mni.8803/nu0.mnc ./tmp.mri_nu_correct.mni.8803/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.8803/0/ -iterations 1000 -distance 50 defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 165. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 170. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 211. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 1051. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 1054. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 1449. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 1455. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 1457. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 1481. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 1631. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 1633. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 1635. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 1637. (Maybe you should just omit the defined()?) defined(@array) is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em line 1639. (Maybe you should just omit the defined()?) [wolff@eber:/scr/eber2/intstats/freesurfer/is09/mri/] [2016-10-17 14:01:41] running: /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 1000 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.8803/0/ ./tmp.mri_nu_correct.mni.8803/nu0.mnc ./tmp.mri_nu_correct.mni.8803/nu1.imp Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Number of iterations: 62 CV of field change: 0.000979967 [wolff@eber:/scr/eber2/intstats/freesurfer/is09/mri/] [2016-10-17 14:03:13] running: /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.8803/nu0.mnc ./tmp.mri_nu_correct.mni.8803/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.8803/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.8803/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /scr/eber2/intstats/freesurfer/is09/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.8803/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.8803/ones.mgz sysname Linux hostname eber machine x86_64 user wolff input ./tmp.mri_nu_correct.mni.8803/nu1.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.8803/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.8803/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.8803/sum.junk --avgwf ./tmp.mri_nu_correct.mni.8803/input.mean.dat $Id: mri_segstats.c,v 1.101 2013/08/20 15:52:54 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.8803/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.8803/sum.junk --avgwf ./tmp.mri_nu_correct.mni.8803/input.mean.dat sysname Linux hostname eber machine x86_64 user wolff UseRobust 0 Loading ./tmp.mri_nu_correct.mni.8803/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.8803/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.8803/ones.mgz --i ./tmp.mri_nu_correct.mni.8803/nu1.mnc --sum ./tmp.mri_nu_correct.mni.8803/sum.junk --avgwf ./tmp.mri_nu_correct.mni.8803/output.mean.dat $Id: mri_segstats.c,v 1.101 2013/08/20 15:52:54 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.8803/ones.mgz --i ./tmp.mri_nu_correct.mni.8803/nu1.mnc --sum ./tmp.mri_nu_correct.mni.8803/sum.junk --avgwf ./tmp.mri_nu_correct.mni.8803/output.mean.dat sysname Linux hostname eber machine x86_64 user wolff UseRobust 0 Loading ./tmp.mri_nu_correct.mni.8803/ones.mgz Loading ./tmp.mri_nu_correct.mni.8803/nu1.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.8803/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.8803/nu1.mnc ./tmp.mri_nu_correct.mni.8803/nu1.mnc mul .91727736055098766296 Saving result to './tmp.mri_nu_correct.mni.8803/nu1.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.8803/nu1.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.8803/nu1.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.8803/nu1.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 12 seconds. mapping ( 8, 165) to ( 3, 110) Mon Oct 17 14:04:12 CEST 2016 mri_nu_correct.mni done mri_add_xform_to_header -c /scr/eber2/intstats/freesurfer/is09/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Mon Oct 17 14:04:14 CEST 2016 /scr/eber2/intstats/freesurfer/is09/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... talairach transform 1.072 0.057 0.001 0.606; -0.050 1.022 0.177 -22.852; 0.004 -0.280 1.191 -3.928; 0.000 0.000 0.000 1.000; processing without aseg, no1d=0 MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 16 Starting OpenSpline(): npoints = 16 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 111 white matter peak found at 109 gm peak at 70 (70), valley at 57 (57) csf peak at 33, setting threshold to 57 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... --------------------------------- 3d normalization pass 2 of 2 white matter peak found at 111 white matter peak found at 110 gm peak at 69 (69), valley at 57 (57) csf peak at 34, setting threshold to 57 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 3 minutes and 20 seconds. #-------------------------------------------- #@# Skull Stripping Mon Oct 17 14:07:35 CEST 2016 /scr/eber2/intstats/freesurfer/is09/mri mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-trusty-amd64/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) ********************************************************* 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=128 y=110 z=134 r=90 first estimation of the main basin volume: 3081494 voxels Looking for seedpoints 2 found in the cerebellum 15 found in the rest of the brain global maximum in x=108, y=104, z=102, Imax=255 CSF=12, 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=18997180062 voxels, voxel volume =1.000 = 18997180062 mmm3 = 18997180.416 cm3 done. PostAnalyze...Basin Prior 63 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=126,y=119, z=128, r=9659 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=21 , nb = 44810 RIGHT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=26 , nb = -1034557482 LEFT_CER CSF_MIN=1, CSF_intensity=2, CSF_MAX=13 , nb = 1074542096 RIGHT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=21 , nb = 1055807990 LEFT_BRAIN CSF_MIN=1, CSF_intensity=2, CSF_MAX=21 , nb = 1079745542 OTHER CSF_MIN=0, CSF_intensity=13, CSF_MAX=34 , nb = -1108861214 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 21, 35, 49, 67 after analyzing : 21, 44, 49, 49 RIGHT_CER before analyzing : 26, 36, 50, 82 after analyzing : 26, 45, 50, 54 LEFT_CER before analyzing : 13, 25, 49, 71 after analyzing : 13, 41, 49, 48 RIGHT_BRAIN before analyzing : 21, 33, 47, 68 after analyzing : 21, 42, 47, 48 LEFT_BRAIN before analyzing : 21, 35, 49, 66 after analyzing : 21, 44, 49, 49 OTHER before analyzing : 34, 42, 49, 67 after analyzing : 34, 46, 49, 51 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...70 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.012 curvature mean = 67.011, std = 7.686 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 1.85, sigma = 3.25 after rotation: sse = 1.85, sigma = 3.25 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 1.94, its var is 2.99 before Erosion-Dilatation 0.24% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...49 iterations mri_strip_skull: done peeling brain Brain Size = 1499113 voxels, voxel volume = 1.000 mm3 = 1499113 mmm3 = 1499.113 cm3 ****************************** Saving brainmask.auto.mgz Keeping edits ... Saving kept edits to brainmask.mgz ..... done INFO: brainmask.mgz already exists! The new brainmask.auto.mgz will not be copied to brainmask.mgz. This is done to retain any edits made to brainmask.mgz. Add the -clean-bm flag to recon-all to overwrite brainmask.mgz. #------------------------------------------ Started at Mon Oct 17 13:58:13 CEST 2016 Ended at Mon Oct 17 14:08:14 CEST 2016 #@#%# recon-all-run-time-hours 0.167 recon-all -s is09 finished without error at Mon Oct 17 14:08:14 CEST 2016 New invocation of recon-all Mon Oct 17 14:11:48 CEST 2016 /scr/eber2/intstats/freesurfer/is09 /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64/bin/recon-all -autorecon1 -nuintensitycor-3T -subjid is09 subjid is09 setenv SUBJECTS_DIR /scr/eber2/intstats/freesurfer FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64 Actual FREESURFER_HOME /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-precise-amd64 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux ren 4.4.0-38-generic #57-Ubuntu SMP Tue Sep 6 15:42:33 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 31775 maxlocks unlimited maxsignal 31775 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 8174060 1285608 4435560 82740 2452892 6471748 Swap: 48829532 0 48829532 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:49-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:50-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:52-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:53-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2016/10/17-12:11:54-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2016/10/17-12:11:54-GMT BuildTimeStamp: Oct 29 2013 21:04:33 CVS: $Id: mri_segstats.c,v 1.101 2013/08/20 15:52:54 greve Exp $ User: maess Machine: ren Platform: Linux PlatformVersion: 4.4.0-38-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /afs/cbs.mpg.de/software/freesurfer/5.3.0/ubuntu-xenial-amd64/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Mon Oct 17 14:11:55 CEST 2016 Found 1 runs /scr/eber2/intstats/freesurfer/is09/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /scr/eber2/intstats/freesurfer/is09/mri/orig/001.mgz /scr/eber2/intstats/freesurfer/is09/mri/rawavg.mgz /scr/eber2/intstats/freesurfer/is09 mri_convert /scr/eber2/intstats/freesurfer/is09/mri/rawavg.mgz /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz --conform mri_convert /scr/eber2/intstats/freesurfer/is09/mri/rawavg.mgz /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /scr/eber2/intstats/freesurfer/is09/mri/rawavg.mgz... TR=2300.00, TE=2.96, TI=900.00, flip angle=9.00 i_ras = (-0, -1, 0) j_ras = (-0, -0, -1) k_ras = (-1, -0, 0) Original Data has (1, 1, 1) mm size and (240, 256, 176) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz... mri_add_xform_to_header -c /scr/eber2/intstats/freesurfer/is09/mri/transforms/talairach.xfm /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz /scr/eber2/intstats/freesurfer/is09/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Oct 17 14:12:13 CEST 2016 /scr/eber2/intstats/freesurfer/is09/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux ren 4.4.0-38-generic #57-Ubuntu SMP Tue Sep 6 15:42:33 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux recon-all -s is09 exited with ERRORS at Mon Oct 17 14:12:21 CEST 2016 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting