Fri May 23 16:00:39 CEST 2014 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41 /usr/local/freesurfer-5.3/bin/recon-all -s 42dd63ba-7ad6-4098-9335-6ecebc46dd41 -i MR000029 subjid 42dd63ba-7ad6-4098-9335-6ecebc46dd41 setenv SUBJECTS_DIR /data-02/camila/subjects_5.3 FREESURFER_HOME /usr/local/freesurfer-5.3 Actual FREESURFER_HOME /usr/local/freesurfer-5.3 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux siv 3.2.0-57-generic #87-Ubuntu SMP Tue Nov 12 21:35:10 UTC 2013 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 386275 maxlocks unlimited maxsignal 386275 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 49460892 49090720 370172 0 3150780 27788704 -/+ buffers/cache: 18151236 31309656 Swap: 9765884 605292 9160592 ######################################## 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: 2014/05/23-14:00:39-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:39-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:39-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:39-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:39-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:39-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:39-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:40-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:40-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:40-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:40-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:40-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:40-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:40-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:40-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:40-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:40-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:40-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:41-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:41-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:41-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:41-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:41-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:41-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:41-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:41-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:41-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:41-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:41-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:42-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:42-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:42-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:42-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:42-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:42-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:42-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:42-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/23-14:00:42-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer-5.3/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer-5.3/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41 mri_convert /data-02/camila/EEG_native_images/ea0cd20d-664c-4a02-948c-f3dc9bb0cec4/MR000029 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig/001.mgz mri_convert /data-02/camila/EEG_native_images/ea0cd20d-664c-4a02-948c-f3dc9bb0cec4/MR000029 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /data-02/camila/EEG_native_images/ea0cd20d-664c-4a02-948c-f3dc9bb0cec4/MR000029... Getting Series No INFO: Found 210 files in /data-02/camila/EEG_native_images/ea0cd20d-664c-4a02-948c-f3dc9bb0cec4 INFO: Scanning for Series Number 11 Scanning Directory INFO: found 208 files in series INFO: loading series header info. RunNo = 10 INFO: sorting. INFO: (256 256 208), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /data-02/camila/EEG_native_images/ea0cd20d-664c-4a02-948c-f3dc9bb0cec4/MR000087 Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName eeg Date and time StudyDate 20121009 StudyTime 154605.203000 SeriesTime 161937.781000 AcqTime 161507.265000 Acquisition parameters PulseSeq *tfl3d1rs_ns Protocol t1_mpr_3d_sag_p2_iso_GD_Siemens PhEncDir ROW EchoNo 1 FlipAngle 9 EchoTime 2.52 InversionTime 900 RepetitionTime 1900 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 10 SeriesNo 11 ImageNo 1 NImageRows 256 NImageCols 256 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 98.3635 168.0625 65.2998 VolRes 1.0000 1.0000 1.0000 VolDim 256 256 208 Vc 0.0029 -1.0000 -0.0000 Vr -0.0207 -0.0001 -0.9998 Vs -0.9998 -0.0029 0.0207 VolCenter -7.9005 39.7567 -60.5159 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) INFO: no Siemens slice order reversal detected (good!). TR=1900.00, TE=2.52, TI=900.00, flip angle=9.00 i_ras = (0.00287277, -0.999996, -1.72014e-08) j_ras = (-0.0207382, -5.9559e-05, -0.999785) k_ras = (-0.999781, -0.00287218, 0.0207382) writing to /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig/001.mgz... #------------------------------------------ Started at Fri May 23 16:00:39 CEST 2014 Ended at Fri May 23 16:01:08 CEST 2014 #@#%# recon-all-run-time-hours 0.008 recon-all -s 42dd63ba-7ad6-4098-9335-6ecebc46dd41 finished without error at Fri May 23 16:01:08 CEST 2014 New invocation of recon-all Tue May 27 10:13:06 CEST 2014 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41 /usr/local/freesurfer-5.3/bin/recon-all -s 42dd63ba-7ad6-4098-9335-6ecebc46dd41 -all -mprage -3T -qcache -hippo-subfields subjid 42dd63ba-7ad6-4098-9335-6ecebc46dd41 setenv SUBJECTS_DIR /data-02/camila/subjects_5.3 FREESURFER_HOME /usr/local/freesurfer-5.3 Actual FREESURFER_HOME /usr/local/freesurfer-5.3 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux siv 3.2.0-57-generic #87-Ubuntu SMP Tue Nov 12 21:35:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 386275 maxlocks unlimited maxsignal 386275 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 49460892 40285372 9175520 0 3052128 17201980 -/+ buffers/cache: 20031264 29429628 Swap: 9765884 640432 9125452 ######################################## 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: 2014/05/27-08:13:06-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:06-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:07-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:07-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:07-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:07-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:07-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:07-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:09-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:09-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:09-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:09-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:09-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:09-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:09-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:10-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:10-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:10-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:10-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:10-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:10-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:10-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:10-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:11-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:11-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:11-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:11-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:11-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:11-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/05/27-08:13:11-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer-5.3/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer-5.3/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Tue May 27 10:13:11 CEST 2014 Found 1 runs /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/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 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig/001.mgz /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/rawavg.mgz /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41 mri_convert /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/rawavg.mgz /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz --conform mri_convert /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/rawavg.mgz /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/rawavg.mgz... TR=1900.00, TE=2.52, TI=900.00, flip angle=9.00 i_ras = (0.00287277, -0.999996, -1.72014e-08) j_ras = (-0.0207382, -5.9559e-05, -0.999785) k_ras = (-0.999781, -0.00287218, 0.0207382) Original Data has (1, 1, 1) mm size and (256, 256, 208) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz... mri_add_xform_to_header -c /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/transforms/talairach.xfm /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue May 27 10:13:27 CEST 2014 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/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 --atlas 3T18yoSchwartzReactN32_as_orig cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue May 27 10:15:53 CEST 2014 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.4235, pval=0.0643 >= threshold=0.0050) awk -f /usr/local/freesurfer-5.3/bin/extract_talairach_avi_QA.awk /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/transforms/talairach_avi.log tal_QC_AZS /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/transforms/talairach_avi.log TalAviQA: 0.92675 z-score: -11 ERROR: Talairach QA check failed! z-score = -11 <= -9 = threshold atlas xform error = 0 < -60 | > 24 Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach INFO: Attempting MINC mritotal to perform Talairach align #-------------------------------------------- #@# Talairach Tue May 27 10:15:53 CEST 2014 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri /usr/local/freesurfer-5.3/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux siv 3.2.0-57-generic #87-Ubuntu SMP Tue Nov 12 21:35:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Tue May 27 10:17:35 CEST 2014 tmpdir is transforms/tmp.talairach.19109 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri mri_convert orig_nu.mgz transforms/tmp.talairach.19109/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.19109/src.mnc $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=1900.00, TE=2.52, TI=900.00, flip angle=9.00 i_ras = (-1, 2.72412e-08, 6.70552e-08) j_ras = (-1.11759e-08, -1.26238e-09, -1) k_ras = (5.72763e-08, 1, -2.40107e-10) writing to transforms/tmp.talairach.19109/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer-5.3/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.19109/src.mnc transforms/talairach.auto.xfm Legacy library shellwords.pl will be removed from the Perl core distribution in the next major release. Please install the separate libperl4-corelibs-perl package. It is being used at /usr/local/freesurfer-5.3/mni/bin/mritotal, line 460. Tue May 27 10:17:52 CEST 2014 talairach done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue May 27 10:17:53 CEST 2014 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0489, pval=0.0034 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux siv 3.2.0-57-generic #87-Ubuntu SMP Tue Nov 12 21:35:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 42dd63ba-7ad6-4098-9335-6ecebc46dd41 exited with ERRORS at Tue May 27 10:17:53 CEST 2014 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Mon Jun 9 16:40:06 CEST 2014 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41 /usr/local/freesurfer-5.3/bin/recon-all -s 42dd63ba-7ad6-4098-9335-6ecebc46dd41 -autorecon1 -mprage -3T -qcache -hippo-subfields subjid 42dd63ba-7ad6-4098-9335-6ecebc46dd41 setenv SUBJECTS_DIR /data-02/camila/subjects_5.3 FREESURFER_HOME /usr/local/freesurfer-5.3 Actual FREESURFER_HOME /usr/local/freesurfer-5.3 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux siv 3.2.0-57-generic #87-Ubuntu SMP Tue Nov 12 21:35:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 386275 maxlocks unlimited maxsignal 386275 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 49460892 35439740 14021152 0 4234724 14447700 -/+ buffers/cache: 16757316 32703576 Swap: 9765884 762348 9003536 ######################################## 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: 2014/06/09-14:40:06-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:06-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:06-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:06-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:06-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:06-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:07-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:07-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:07-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:07-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:07-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:07-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:07-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:07-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:07-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:07-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:09-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:09-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:09-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:09-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:09-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:09-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:09-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:09-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:09-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:09-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/09-14:40:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer-5.3/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer-5.3/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Mon Jun 9 16:40:10 CEST 2014 Found 1 runs /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/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 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig/001.mgz /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/rawavg.mgz /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41 mri_convert /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/rawavg.mgz /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz --conform mri_convert /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/rawavg.mgz /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/rawavg.mgz... TR=1900.00, TE=2.52, TI=900.00, flip angle=9.00 i_ras = (0.00287277, -0.999996, -1.72014e-08) j_ras = (-0.0207382, -5.9559e-05, -0.999785) k_ras = (-0.999781, -0.00287218, 0.0207382) Original Data has (1, 1, 1) mm size and (256, 256, 208) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz... mri_add_xform_to_header -c /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/transforms/talairach.xfm /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Jun 9 16:40:27 CEST 2014 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/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 --atlas 3T18yoSchwartzReactN32_as_orig 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 Jun 9 16:42:59 CEST 2014 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.3838, pval=0.0643 >= threshold=0.0050) awk -f /usr/local/freesurfer-5.3/bin/extract_talairach_avi_QA.awk /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/transforms/talairach_avi.log tal_QC_AZS /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/transforms/talairach_avi.log TalAviQA: 0.92675 z-score: -11 ERROR: Talairach QA check failed! z-score = -11 <= -9 = threshold atlas xform error = 0 < -60 | > 24 Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach INFO: Attempting MINC mritotal to perform Talairach align #-------------------------------------------- #@# Talairach Mon Jun 9 16:43:00 CEST 2014 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri /usr/local/freesurfer-5.3/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux siv 3.2.0-57-generic #87-Ubuntu SMP Tue Nov 12 21:35:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Mon Jun 9 16:44:42 CEST 2014 tmpdir is transforms/tmp.talairach.8260 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri mri_convert orig_nu.mgz transforms/tmp.talairach.8260/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.8260/src.mnc $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=1900.00, TE=2.52, TI=900.00, flip angle=9.00 i_ras = (-1, 2.72412e-08, 6.70552e-08) j_ras = (-1.11759e-08, -1.26238e-09, -1) k_ras = (5.72763e-08, 1, -2.40107e-10) writing to transforms/tmp.talairach.8260/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer-5.3/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.8260/src.mnc transforms/talairach.auto.xfm Legacy library shellwords.pl will be removed from the Perl core distribution in the next major release. Please install the separate libperl4-corelibs-perl package. It is being used at /usr/local/freesurfer-5.3/mni/bin/mritotal, line 460. Mon Jun 9 16:44:58 CEST 2014 talairach done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Mon Jun 9 16:44:59 CEST 2014 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0489, pval=0.0034 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux siv 3.2.0-57-generic #87-Ubuntu SMP Tue Nov 12 21:35:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 42dd63ba-7ad6-4098-9335-6ecebc46dd41 exited with ERRORS at Mon Jun 9 16:44:59 CEST 2014 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Tue Jun 10 09:35:36 CEST 2014 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41 /usr/local/freesurfer-5.3/bin/recon-all -s 42dd63ba-7ad6-4098-9335-6ecebc46dd41 -autorecon1 -notal-check -mprage -3T -qcache -hippo-subfields subjid 42dd63ba-7ad6-4098-9335-6ecebc46dd41 setenv SUBJECTS_DIR /data-02/camila/subjects_5.3 FREESURFER_HOME /usr/local/freesurfer-5.3 Actual FREESURFER_HOME /usr/local/freesurfer-5.3 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux siv 3.2.0-57-generic #87-Ubuntu SMP Tue Nov 12 21:35:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 386275 maxlocks unlimited maxsignal 386275 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 49460892 37037716 12423176 0 4296296 23676164 -/+ buffers/cache: 9065256 40395636 Swap: 9765884 61144 9704740 ######################################## 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: 2014/06/10-07:35:36-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:36-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:36-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:36-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:36-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:36-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:36-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:36-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:37-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:37-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:37-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:37-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:37-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:37-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:37-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:37-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:37-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:37-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:37-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:38-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:38-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:38-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:38-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:38-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:38-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:38-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:38-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:38-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:38-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:38-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:38-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:39-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:39-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:39-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:39-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:39-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:39-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/06/10-07:35:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-57-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer-5.3/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer-5.3/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Tue Jun 10 09:35:39 CEST 2014 Found 1 runs /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/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 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig/001.mgz /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/rawavg.mgz /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41 mri_convert /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/rawavg.mgz /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz --conform mri_convert /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/rawavg.mgz /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/rawavg.mgz... TR=1900.00, TE=2.52, TI=900.00, flip angle=9.00 i_ras = (0.00287277, -0.999996, -1.72014e-08) j_ras = (-0.0207382, -5.9559e-05, -0.999785) k_ras = (-0.999781, -0.00287218, 0.0207382) Original Data has (1, 1, 1) mm size and (256, 256, 208) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz... mri_add_xform_to_header -c /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/transforms/talairach.xfm /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue Jun 10 09:35:55 CEST 2014 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/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 --atlas 3T18yoSchwartzReactN32_as_orig 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 #-------------------------------------------- #@# Nu Intensity Correction Tue Jun 10 09:38:11 CEST 2014 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --proto-iters 1000 --distance 50 --n 1 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri /usr/local/freesurfer-5.3/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 siv 3.2.0-57-generic #87-Ubuntu SMP Tue Nov 12 21:35:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Tue Jun 10 09:38:11 CEST 2014 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 tmpdir is ./tmp.mri_nu_correct.mni.5723 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.5723/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.5723/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=1900.00, TE=2.52, TI=900.00, flip angle=9.00 i_ras = (-1, 2.72412e-08, 6.70552e-08) j_ras = (-1.11759e-08, -1.26238e-09, -1) k_ras = (5.72763e-08, 1, -2.40107e-10) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.5723/nu0.mnc... -------------------------------------------------------- Iteration 1 Tue Jun 10 09:38:13 CEST 2014 nu_correct -clobber ./tmp.mri_nu_correct.mni.5723/nu0.mnc ./tmp.mri_nu_correct.mni.5723/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.5723/0/ -iterations 1000 -distance 50 [camila@siv:/data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/] [2014-06-10 09:38:13] running: /usr/local/freesurfer-5.3/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.5723/0/ ./tmp.mri_nu_correct.mni.5723/nu0.mnc ./tmp.mri_nu_correct.mni.5723/nu1.imp Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer-5.3/mni/bin/sharpen_volume line 153. Processing:.................................................................Done Use of ?PATTERN? without explicit operator is deprecated at /usr/local/freesurfer-5.3/mni/bin/sharpen_volume line 153. 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Processing:.................................................................Done Number of iterations: 64 CV of field change: 0.000990255 [camila@siv:/data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/] [2014-06-10 09:39:36] running: /usr/local/freesurfer-5.3/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.5723/nu0.mnc ./tmp.mri_nu_correct.mni.5723/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.5723/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.5723/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.5723/nu1.mnc --min -1 --o ./tmp.mri_nu_correct.mni.5723/ones.mgz sysname Linux hostname siv machine x86_64 user camila input ./tmp.mri_nu_correct.mni.5723/nu1.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.5723/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.5723/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.5723/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5723/input.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5723/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.5723/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5723/input.mean.dat sysname Linux hostname siv machine x86_64 user camila UseRobust 0 Loading ./tmp.mri_nu_correct.mni.5723/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.5723/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5723/ones.mgz --i ./tmp.mri_nu_correct.mni.5723/nu1.mnc --sum ./tmp.mri_nu_correct.mni.5723/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5723/output.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.5723/ones.mgz --i ./tmp.mri_nu_correct.mni.5723/nu1.mnc --sum ./tmp.mri_nu_correct.mni.5723/sum.junk --avgwf ./tmp.mri_nu_correct.mni.5723/output.mean.dat sysname Linux hostname siv machine x86_64 user camila UseRobust 0 Loading ./tmp.mri_nu_correct.mni.5723/ones.mgz Loading ./tmp.mri_nu_correct.mni.5723/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.5723/output.mean.dat mri_segstats done mris_calc -o ./tmp.mri_nu_correct.mni.5723/nu1.mnc ./tmp.mri_nu_correct.mni.5723/nu1.mnc mul 1.02960885229598929857 Saving result to './tmp.mri_nu_correct.mni.5723/nu1.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.5723/nu1.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.5723/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.5723/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 2.72412e-08, 6.70552e-08) j_ras = (-1.11759e-08, -1.26238e-09, -1) k_ras = (5.72763e-08, 1, -2.40107e-10) INFO: transform src into the like-volume: orig.mgz writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 8 seconds. mapping ( 5, 138) to ( 3, 110) Tue Jun 10 09:40:22 CEST 2014 mri_nu_correct.mni done mri_add_xform_to_header -c /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/transforms/talairach.xfm nu.mgz nu.mgz INFO: extension is mgz #-------------------------------------------- #@# Intensity Normalization Tue Jun 10 09:40:23 CEST 2014 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri mri_normalize -g 1 -mprage nu.mgz T1.mgz using max gradient = 1.000 assuming input volume is MGH (Van der Kouwe) MP-RAGE reading from nu.mgz... normalizing image... talairach transform 0.778 0.093 0.008 4.233; -0.085 0.742 -0.397 -78.514; -0.062 0.440 0.835 59.869; 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 = 19 Starting OpenSpline(): npoints = 19 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 99 gm peak at 69 (69), valley at 22 (22) csf peak at 16, setting threshold to 51 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 77 (77), valley at 21 (21) csf peak at 16, setting threshold to 56 building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Done iterating --------------------------------- writing output to T1.mgz 3D bias adjustment took 2 minutes and 37 seconds. #-------------------------------------------- #@# Skull Stripping Tue Jun 10 09:43:01 CEST 2014 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri mri_em_register -skull nu.mgz /usr/local/freesurfer-5.3/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta ======= NUMBER OF OPENMP THREADS = 1 ======= aligning to atlas containing skull, setting unknown_nbr_spacing = 5 reading 1 input volumes... logging results to talairach_with_skull.log reading '/usr/local/freesurfer-5.3/average/RB_all_withskull_2008-03-26.gca'... average std = 23.1 using min determinant for regularization = 53.4 0 singular and 5702 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 20.2 or > 943.7 total sample mean = 92.0 (1443 zeros) ************************************************ spacing=8, using 3481 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=8.0 skull bounding box = (50, 10, 9) --> (203, 255, 243) using (101, 92, 126) as brain centroid... mean wm in atlas = 126, using box (82,62,97) --> (119, 122,154) to find MRI wm before smoothing, mri peak at 68 after smoothing, mri peak at 67, scaling input intensities by 1.881 scaling channel 0 by 1.8806 initial log_p = -4.8 ************************************************ First Search limited to translation only. ************************************************ max log p = -4.821758 @ (9.091, 9.091, -9.091) max log p = -4.700859 @ (-13.636, 13.636, 4.545) max log p = -4.636461 @ (2.273, 2.273, -2.273) max log p = -4.636461 @ (0.000, 0.000, 0.000) max log p = -4.612874 @ (0.568, -0.568, 0.568) max log p = -4.612874 @ (0.000, 0.000, 0.000) Found translation: (-1.7, 24.4, -6.3): log p = -4.613 **************************************** Nine parameter search. iteration 0 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.4, old_max_log_p =-4.6 (thresh=-4.6) 1.075 0.000 0.000 -11.264; 0.000 1.142 0.473 -34.932; 0.000 -0.407 0.983 42.540; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 1 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.4, old_max_log_p =-4.4 (thresh=-4.4) 1.075 0.000 0.000 -11.264; 0.000 1.142 0.473 -34.932; 0.000 -0.377 0.909 47.302; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 2 nscales = 0 ... **************************************** Result so far: scale 1.000: max_log_p=-4.4, old_max_log_p =-4.4 (thresh=-4.4) 1.075 0.000 0.000 -11.264; 0.000 1.142 0.473 -34.932; 0.000 -0.377 0.909 47.302; 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=-4.3, old_max_log_p =-4.4 (thresh=-4.4) 1.131 -0.060 -0.093 -3.204; 0.073 1.152 0.439 -37.882; 0.071 -0.350 0.957 30.658; 0.000 0.000 0.000 1.000; **************************************** Nine parameter search. iteration 4 nscales = 1 ... **************************************** Result so far: scale 0.250: max_log_p=-4.3, old_max_log_p =-4.3 (thresh=-4.3) 1.131 -0.060 -0.093 -3.204; 0.073 1.152 0.439 -37.882; 0.071 -0.350 0.957 30.658; 0.000 0.000 0.000 1.000; reducing scale to 0.0625 **************************************** Nine parameter search. iteration 5 nscales = 2 ... **************************************** Result so far: scale 0.062: max_log_p=-4.3, old_max_log_p =-4.3 (thresh=-4.3) 1.131 -0.060 -0.093 -3.204; 0.073 1.154 0.440 -38.068; 0.071 -0.350 0.957 30.658; 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 1.13136 -0.05972 -0.09323 -3.20387; 0.07259 1.15365 0.43980 -38.06790; 0.07061 -0.34955 0.95730 30.65839; 0.00000 0.00000 0.00000 1.00000; nsamples 3481 Quasinewton: input matrix 1.13136 -0.05972 -0.09323 -3.20387; 0.07259 1.15365 0.43980 -38.06790; 0.07061 -0.34955 0.95730 30.65839; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 4 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 008: -log(p) = -0.0 tol 0.000010 Resulting transform: 1.131 -0.060 -0.093 -3.204; 0.073 1.154 0.440 -38.068; 0.071 -0.350 0.957 30.658; 0.000 0.000 0.000 1.000; pass 1, spacing 8: log(p) = -4.3 (old=-4.8) transform before final EM align: 1.131 -0.060 -0.093 -3.204; 0.073 1.154 0.440 -38.068; 0.071 -0.350 0.957 30.658; 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 1.13136 -0.05972 -0.09323 -3.20387; 0.07259 1.15365 0.43980 -38.06790; 0.07061 -0.34955 0.95730 30.65839; 0.00000 0.00000 0.00000 1.00000; nsamples 382743 Quasinewton: input matrix 1.13136 -0.05972 -0.09323 -3.20387; 0.07259 1.15365 0.43980 -38.06790; 0.07061 -0.34955 0.95730 30.65839; 0.00000 0.00000 0.00000 1.00000; IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESoutof QuasiNewtonEMA: 010: -log(p) = 4.7 tol 0.000000 final transform: 1.131 -0.060 -0.093 -3.204; 0.073 1.154 0.440 -38.068; 0.071 -0.350 0.957 30.658; 0.000 0.000 0.000 1.000; writing output transformation to transforms/talairach_with_skull.lta... registration took 25 minutes and 5 seconds. mri_watershed -T1 -brain_atlas /usr/local/freesurfer-5.3/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=127 y=110 z=106 r=94 first estimation of the main basin volume: 3588655 voxels Looking for seedpoints 2 found in the cerebellum 16 found in the rest of the brain global maximum in x=104, y=69, z=80, Imax=255 CSF=20, 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=21777539697 voxels, voxel volume =1.000 = 21777539697 mmm3 = 21777539.072 cm3 done. PostAnalyze...Basin Prior 1152 basins merged thanks to atlas ambiguous basin, merged: at least 21 ambiguous voxels; size: 8927 voxels ***** 1 basin(s) merged in 2 iteration(s) ***** 8927 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=127,y=95, z=100, r=10164 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=23, CSF_MAX=77 , nb = 37934 RIGHT_CER CSF_MIN=7, CSF_intensity=27, CSF_MAX=63 , nb = -1028018881 LEFT_CER CSF_MIN=1, CSF_intensity=25, CSF_MAX=70 , nb = 1090288902 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=20, CSF_MAX=74 , nb = -1060775971 LEFT_BRAIN CSF_MIN=0, CSF_intensity=23, CSF_MAX=82 , nb = 1067415870 OTHER CSF_MIN=0, CSF_intensity=4, CSF_MAX=62 , nb = 1076942966 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 77, 57, 47, 77 after analyzing : 48, 57, 57, 62 RIGHT_CER before analyzing : 63, 55, 48, 82 after analyzing : 45, 55, 55, 61 LEFT_CER before analyzing : 70, 55, 44, 80 after analyzing : 44, 55, 55, 61 RIGHT_BRAIN before analyzing : 74, 56, 47, 77 after analyzing : 47, 56, 56, 61 LEFT_BRAIN before analyzing : 82, 59, 47, 78 after analyzing : 49, 59, 59, 63 OTHER before analyzing : 62, 69, 73, 95 after analyzing : 62, 71, 73, 77 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...73 iterations *********************VALIDATION********************* curvature mean = -0.013, std = 0.011 curvature mean = 68.991, std = 9.036 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 7.48, sigma = 17.92 after rotation: sse = 7.48, sigma = 17.92 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 10.81, its var is 20.84 before Erosion-Dilatation 10.12% of inacurate vertices after Erosion-Dilatation 14.60% 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...40 iterations mri_strip_skull: done peeling brain Brain Size = 1635083 voxels, voxel volume = 1.000 mm3 = 1635083 mmm3 = 1635.083 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/surf #-------------------------------------------- #@# Qdec Cache lh thickness fsaverage Tue Jun 10 10:08:34 CEST 2014 INFO: File lh.thickness does not exist! Skipping creation of smoothed data for lh.thickness #-------------------------------------------- #@# Qdec Cache lh area fsaverage Tue Jun 10 10:08:34 CEST 2014 INFO: File lh.area does not exist! Skipping creation of smoothed data for lh.area #-------------------------------------------- #@# Qdec Cache lh area.pial fsaverage Tue Jun 10 10:08:34 CEST 2014 INFO: File lh.area.pial does not exist! Skipping creation of smoothed data for lh.area.pial #-------------------------------------------- #@# Qdec Cache lh volume fsaverage Tue Jun 10 10:08:34 CEST 2014 INFO: File lh.volume does not exist! Skipping creation of smoothed data for lh.volume #-------------------------------------------- #@# Qdec Cache lh curv fsaverage Tue Jun 10 10:08:34 CEST 2014 INFO: File lh.curv does not exist! Skipping creation of smoothed data for lh.curv #-------------------------------------------- #@# Qdec Cache lh sulc fsaverage Tue Jun 10 10:08:34 CEST 2014 INFO: File lh.sulc does not exist! Skipping creation of smoothed data for lh.sulc #-------------------------------------------- #@# Qdec Cache lh white.K fsaverage Tue Jun 10 10:08:34 CEST 2014 INFO: File lh.white.K does not exist! Skipping creation of smoothed data for lh.white.K #-------------------------------------------- #@# Qdec Cache lh white.H fsaverage Tue Jun 10 10:08:34 CEST 2014 INFO: File lh.white.H does not exist! Skipping creation of smoothed data for lh.white.H #-------------------------------------------- #@# Qdec Cache lh jacobian_white fsaverage Tue Jun 10 10:08:34 CEST 2014 INFO: File lh.jacobian_white does not exist! Skipping creation of smoothed data for lh.jacobian_white #-------------------------------------------- #@# Qdec Cache lh w-g.pct.mgh fsaverage Tue Jun 10 10:08:34 CEST 2014 INFO: File lh.w-g.pct.mgh does not exist! Skipping creation of smoothed data for lh.w-g.pct.mgh #-------------------------------------------- #@# Qdec Cache rh thickness fsaverage Tue Jun 10 10:08:34 CEST 2014 INFO: File rh.thickness does not exist! Skipping creation of smoothed data for rh.thickness #-------------------------------------------- #@# Qdec Cache rh area fsaverage Tue Jun 10 10:08:34 CEST 2014 INFO: File rh.area does not exist! Skipping creation of smoothed data for rh.area #-------------------------------------------- #@# Qdec Cache rh area.pial fsaverage Tue Jun 10 10:08:34 CEST 2014 INFO: File rh.area.pial does not exist! Skipping creation of smoothed data for rh.area.pial #-------------------------------------------- #@# Qdec Cache rh volume fsaverage Tue Jun 10 10:08:34 CEST 2014 INFO: File rh.volume does not exist! Skipping creation of smoothed data for rh.volume #-------------------------------------------- #@# Qdec Cache rh curv fsaverage Tue Jun 10 10:08:34 CEST 2014 INFO: File rh.curv does not exist! Skipping creation of smoothed data for rh.curv #-------------------------------------------- #@# Qdec Cache rh sulc fsaverage Tue Jun 10 10:08:34 CEST 2014 INFO: File rh.sulc does not exist! Skipping creation of smoothed data for rh.sulc #-------------------------------------------- #@# Qdec Cache rh white.K fsaverage Tue Jun 10 10:08:34 CEST 2014 INFO: File rh.white.K does not exist! Skipping creation of smoothed data for rh.white.K #-------------------------------------------- #@# Qdec Cache rh white.H fsaverage Tue Jun 10 10:08:34 CEST 2014 INFO: File rh.white.H does not exist! Skipping creation of smoothed data for rh.white.H #-------------------------------------------- #@# Qdec Cache rh jacobian_white fsaverage Tue Jun 10 10:08:34 CEST 2014 INFO: File rh.jacobian_white does not exist! Skipping creation of smoothed data for rh.jacobian_white #-------------------------------------------- #@# Qdec Cache rh w-g.pct.mgh fsaverage Tue Jun 10 10:08:34 CEST 2014 INFO: File rh.w-g.pct.mgh does not exist! Skipping creation of smoothed data for rh.w-g.pct.mgh #-------------------------------------------- #@# Hippocampal Subfields processing Tue Jun 10 10:08:34 CEST 2014 Linux siv 3.2.0-57-generic #87-Ubuntu SMP Tue Nov 12 21:35:10 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 42dd63ba-7ad6-4098-9335-6ecebc46dd41 exited with ERRORS at Tue Jun 10 10:08:34 CEST 2014 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Tue Jul 22 15:57:06 CEST 2014 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41 /usr/local/freesurfer-5.3/bin/recon-all -s 42dd63ba-7ad6-4098-9335-6ecebc46dd41 -autorecon1 -clean-tal -mprage -3T -qcache -hippo-subfields subjid 42dd63ba-7ad6-4098-9335-6ecebc46dd41 setenv SUBJECTS_DIR /data-02/camila/subjects_5.3 FREESURFER_HOME /usr/local/freesurfer-5.3 Actual FREESURFER_HOME /usr/local/freesurfer-5.3 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux siv 3.2.0-65-generic #99-Ubuntu SMP Fri Jul 4 21:03:29 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 386275 maxlocks unlimited maxsignal 386275 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buffers cached Mem: 49460880 48074516 1386364 0 1083276 39345188 -/+ buffers/cache: 7646052 41814828 Swap: 9765884 148436 9617448 ######################################## 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: 2014/07/22-13:57:06-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:06-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:06-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:06-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:06-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:06-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:06-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:07-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:07-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:07-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:07-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:07-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:07-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:07-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:07-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:07-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:07-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:08-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:09-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:09-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:09-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:09-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:09-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:09-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:09-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:09-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:09-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: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/07/22-13:57:09-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: camila Machine: siv Platform: Linux PlatformVersion: 3.2.0-65-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer-5.3/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer-5.3/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### mv -f /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/transforms/talairach.xfm /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/trash #-------------------------------------------- #@# MotionCor Tue Jul 22 15:57:09 CEST 2014 Found 1 runs /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/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 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig/001.mgz /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/rawavg.mgz /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41 mri_convert /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/rawavg.mgz /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz --conform mri_convert /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/rawavg.mgz /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/rawavg.mgz... TR=1900.00, TE=2.52, TI=900.00, flip angle=9.00 i_ras = (0.00287277, -0.999996, -1.72014e-08) j_ras = (-0.0207382, -5.9559e-05, -0.999785) k_ras = (-0.999781, -0.00287218, 0.0207382) Original Data has (1, 1, 1) mm size and (256, 256, 208) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz... mri_add_xform_to_header -c /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/transforms/talairach.xfm /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Tue Jul 22 15:57:28 CEST 2014 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/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 --atlas 3T18yoSchwartzReactN32_as_orig cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue Jul 22 15:59:58 CEST 2014 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.4235, pval=0.0643 >= threshold=0.0050) awk -f /usr/local/freesurfer-5.3/bin/extract_talairach_avi_QA.awk /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/transforms/talairach_avi.log tal_QC_AZS /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/transforms/talairach_avi.log TalAviQA: 0.92675 z-score: -11 ERROR: Talairach QA check failed! z-score = -11 <= -9 = threshold atlas xform error = 0 < -60 | > 24 Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach INFO: Attempting MINC mritotal to perform Talairach align #-------------------------------------------- #@# Talairach Tue Jul 22 15:59:58 CEST 2014 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri /usr/local/freesurfer-5.3/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux siv 3.2.0-65-generic #99-Ubuntu SMP Fri Jul 4 21:03:29 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Tue Jul 22 16:01:39 CEST 2014 tmpdir is transforms/tmp.talairach.32005 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri mri_convert orig_nu.mgz transforms/tmp.talairach.32005/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.32005/src.mnc $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=1900.00, TE=2.52, TI=900.00, flip angle=9.00 i_ras = (-1, 2.72412e-08, 6.70552e-08) j_ras = (-1.11759e-08, -1.26238e-09, -1) k_ras = (5.72763e-08, 1, -2.40107e-10) writing to transforms/tmp.talairach.32005/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer-5.3/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.32005/src.mnc transforms/talairach.auto.xfm Legacy library shellwords.pl will be removed from the Perl core distribution in the next major release. Please install the separate libperl4-corelibs-perl package. It is being used at /usr/local/freesurfer-5.3/mni/bin/mritotal, line 460. Tue Jul 22 16:01:56 CEST 2014 talairach done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue Jul 22 16:01:57 CEST 2014 /data-02/camila/subjects_5.3/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0489, pval=0.0034 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux siv 3.2.0-65-generic #99-Ubuntu SMP Fri Jul 4 21:03:29 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 42dd63ba-7ad6-4098-9335-6ecebc46dd41 exited with ERRORS at Tue Jul 22 16:01:57 CEST 2014 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all tor 9 feb 2017 16:00:04 CET /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41 /usr/local/freesurfer-5.3.0/bin/recon-all -all -subjid 42dd63ba-7ad6-4098-9335-6ecebc46dd41 subjid 42dd63ba-7ad6-4098-9335-6ecebc46dd41 setenv SUBJECTS_DIR /data-02/teodora/FreeSurfer FREESURFER_HOME /usr/local/freesurfer-5.3.0 Actual FREESURFER_HOME /usr/local/freesurfer-5.3.0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux siv 4.4.0-62-generic #83-Ubuntu SMP Wed Jan 18 14:10:15 UTC 2017 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 257137 maxlocks unlimited maxsignal 257137 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 65931128 6781088 337040 260564 58813000 58241776 Swap: 15625212 696556 14928656 ######################################## 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: 2017/02/09-15:00:04-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-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: 2017/02/09-15:00:05-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-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: 2017/02/09-15:00:05-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:05-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:05-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:05-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:05-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:06-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:06-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:06-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:06-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:06-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:06-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:07-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:07-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:07-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:07-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:07-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:07-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:07-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:08-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:08-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:08-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:08-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:08-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:08-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:08-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:09-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:09-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:09-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:09-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:09-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-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: 2017/02/09-15:00:09-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-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: 2017/02/09-15:00:10-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:10-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:10-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:10-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/09-15:00:10-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer-5.3.0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer-5.3.0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer-5.3.0 Previous: /usr/local/freesurfer-5.3 #-------------------------------------------- #@# MotionCor tor 9 feb 2017 16:00:11 CET Found 1 runs /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/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 /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig/001.mgz /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/rawavg.mgz /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41 mri_convert /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/rawavg.mgz /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz --conform mri_convert /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/rawavg.mgz /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/rawavg.mgz... TR=1900.00, TE=2.52, TI=900.00, flip angle=9.00 i_ras = (0.00287277, -0.999996, -1.72014e-08) j_ras = (-0.0207382, -5.9559e-05, -0.999785) k_ras = (-0.999781, -0.00287218, 0.0207382) Original Data has (1, 1, 1) mm size and (256, 256, 208) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz... mri_add_xform_to_header -c /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/transforms/talairach.xfm /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach tor 9 feb 2017 16:00:25 CET /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux siv 4.4.0-62-generic #83-Ubuntu SMP Wed Jan 18 14:10:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 42dd63ba-7ad6-4098-9335-6ecebc46dd41 exited with ERRORS at tor 9 feb 2017 16:00:28 CET To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all tor 16 feb 2017 11:08:48 CET /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41 /usr/local/freesurfer-5.3.0/bin/recon-all -all -subjid 42dd63ba-7ad6-4098-9335-6ecebc46dd41 subjid 42dd63ba-7ad6-4098-9335-6ecebc46dd41 setenv SUBJECTS_DIR /data-02/teodora/FreeSurfer FREESURFER_HOME /usr/local/freesurfer-5.3.0 Actual FREESURFER_HOME /usr/local/freesurfer-5.3.0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux siv 4.4.0-62-generic #83-Ubuntu SMP Wed Jan 18 14:10:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 257137 maxlocks unlimited maxsignal 257137 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 65931128 5415328 45259272 287152 15256528 59568956 Swap: 15625212 1146744 14478468 ######################################## 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: 2017/02/16-10:08:48-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-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: 2017/02/16-10:08:48-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-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: 2017/02/16-10:08:48-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:48-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:48-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:48-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:48-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:48-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:48-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:49-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:49-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:49-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:49-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:49-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:49-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:49-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:49-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:49-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:49-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:49-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:49-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:49-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:50-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:50-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:50-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:50-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:50-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:50-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:50-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:50-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:50-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:50-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-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: 2017/02/16-10:08:50-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-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: 2017/02/16-10:08:50-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:50-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:51-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:51-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: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/02/16-10:08:51-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: teodora Machine: siv Platform: Linux PlatformVersion: 4.4.0-62-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer-5.3.0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer-5.3.0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer-5.3.0 Previous: /usr/local/freesurfer-5.3 #-------------------------------------------- #@# MotionCor tor 16 feb 2017 11:08:52 CET Found 1 runs /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/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 /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig/001.mgz /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/rawavg.mgz /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41 mri_convert /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/rawavg.mgz /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz --conform mri_convert /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/rawavg.mgz /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/rawavg.mgz... TR=1900.00, TE=2.52, TI=900.00, flip angle=9.00 i_ras = (0.00287277, -0.999996, -1.72014e-08) j_ras = (-0.0207382, -5.9559e-05, -0.999785) k_ras = (-0.999781, -0.00287218, 0.0207382) Original Data has (1, 1, 1) mm size and (256, 256, 208) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz... mri_add_xform_to_header -c /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/transforms/talairach.xfm /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach tor 16 feb 2017 11:09:05 CET /data-02/teodora/FreeSurfer/42dd63ba-7ad6-4098-9335-6ecebc46dd41/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux siv 4.4.0-62-generic #83-Ubuntu SMP Wed Jan 18 14:10:15 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 42dd63ba-7ad6-4098-9335-6ecebc46dd41 exited with ERRORS at tor 16 feb 2017 11:09:08 CET To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting