Wed Aug 9 14:00:12 EDT 2017 /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error /home/lab/Desktop/freesurfer/bin/recon-all -i sub-09_run-01_T1w.nii.gz -s sub-09-AW-error -all subjid sub-09-AW-error setenv SUBJECTS_DIR /home/lab/Desktop/freesurfer/subjects FREESURFER_HOME /home/lab/Desktop/freesurfer Actual FREESURFER_HOME /home/lab/Desktop/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux lab-ThinkStation-E31 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 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 15345 maxlocks unlimited maxsignal 15345 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 3973012 799656 2110992 15944 1062364 2803244 Swap: 4121596 730532 3391064 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:13-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:14-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/09-18:00:14-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:14-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/09-18:00:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/09-18:00:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/09-18:00:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/09-18:00:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/09-18:00:15-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/09-18:00:16-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:16-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:16-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/09-18:00:16-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:16-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:16-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:16-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:17-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:17-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:17-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/09-18:00:17-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:17-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:17-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:18-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/09-18:00:18-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:18-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2017/08/09-18:00:18-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:18-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:18-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:19-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:19-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:19-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:19-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:19-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:19-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:20-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:20-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2017/08/09-18:00:20-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: lab Machine: lab-ThinkStation-E31 Platform: Linux PlatformVersion: 4.10.0-28-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /home/lab/Desktop/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /home/lab/Desktop/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error mri_convert /home/lab/Desktop/freesurfer/subjects/sub-09_run-01_T1w.nii.gz /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri/orig/001.mgz mri_convert.bin /home/lab/Desktop/freesurfer/subjects/sub-09_run-01_T1w.nii.gz /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/lab/Desktop/freesurfer/subjects/sub-09_run-01_T1w.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Wed Aug 9 14:00:23 EDT 2017 Found 1 runs /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/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 /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri/orig/001.mgz /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri/rawavg.mgz /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error mri_convert /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri/rawavg.mgz /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri/orig.mgz --conform mri_convert.bin /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri/rawavg.mgz /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri/orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri/orig.mgz... mri_add_xform_to_header -c /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri/transforms/talairach.xfm /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri/orig.mgz /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Wed Aug 9 14:00:33 EDT 2017 /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri /home/lab/Desktop/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux lab-ThinkStation-E31 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Wed Aug 9 14:00:33 EDT 2017 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.9657 /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9657/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.9657/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.9657/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Aug 9 14:00:34 EDT 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.9657/nu0.mnc ./tmp.mri_nu_correct.mni.9657/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.9657/0/ -iterations 1000 -distance 50 [lab@lab-ThinkStation-E31:/home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri/] [2017-08-09 14:00:35] running: /home/lab/Desktop/freesurfer/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 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.9657/0/ ./tmp.mri_nu_correct.mni.9657/nu0.mnc ./tmp.mri_nu_correct.mni.9657/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 10 CV of field change: 0.000937421 mri_convert ./tmp.mri_nu_correct.mni.9657/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.9657/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.9657/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Wed Aug 9 14:01:05 EDT 2017 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm talairach_avi log file is transforms/talairach_avi.log... Started at Wed Aug 9 14:01:05 EDT 2017 Ended at Wed Aug 9 14:01:53 EDT 2017 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Wed Aug 9 14:01:55 EDT 2017 /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < 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 INFO: Retrying Talairach align using 3T-based atlas... #-------------------------------------------- #@# Talairach Wed Aug 9 14:01:55 EDT 2017 /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri /home/lab/Desktop/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux lab-ThinkStation-E31 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Wed Aug 9 14:01:55 EDT 2017 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.10032 /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10032/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.10032/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.10032/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Aug 9 14:01:56 EDT 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.10032/nu0.mnc ./tmp.mri_nu_correct.mni.10032/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.10032/0/ -iterations 1000 -distance 50 [lab@lab-ThinkStation-E31:/home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri/] [2017-08-09 14:01:56] running: /home/lab/Desktop/freesurfer/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 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.10032/0/ ./tmp.mri_nu_correct.mni.10032/nu0.mnc ./tmp.mri_nu_correct.mni.10032/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 10 CV of field change: 0.000937421 mri_convert ./tmp.mri_nu_correct.mni.10032/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.10032/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.10032/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Wed Aug 9 14:02:25 EDT 2017 mri_nu_correct.mni done talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig talairach_avi log file is transforms/talairach_avi.log... Started at Wed Aug 9 14:02:25 EDT 2017 Ended at Wed Aug 9 14:03:10 EDT 2017 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Wed Aug 9 14:03:12 EDT 2017 /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0389, 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 INFO: Trying MINC mritotal to perform Talairach align... #-------------------------------------------- #@# Talairach Wed Aug 9 14:03:12 EDT 2017 /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri /home/lab/Desktop/freesurfer/bin/mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 nIters 1 $Id: mri_nu_correct.mni,v 1.27 2016/02/26 16:19:49 mreuter Exp $ Linux lab-ThinkStation-E31 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Wed Aug 9 14:03:12 EDT 2017 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.10399 /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10399/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.10399/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.10399/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Aug 9 14:03:14 EDT 2017 nu_correct -clobber ./tmp.mri_nu_correct.mni.10399/nu0.mnc ./tmp.mri_nu_correct.mni.10399/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.10399/0/ -iterations 1000 -distance 50 [lab@lab-ThinkStation-E31:/home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri/] [2017-08-09 14:03:14] running: /home/lab/Desktop/freesurfer/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 1.0e-7 -distance 50 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.10399/0/ ./tmp.mri_nu_correct.mni.10399/nu0.mnc ./tmp.mri_nu_correct.mni.10399/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 10 CV of field change: 0.000937421 mri_convert ./tmp.mri_nu_correct.mni.10399/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.10399/nu1.mnc orig_nu.mgz --like orig.mgz --conform $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.10399/nu1.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) INFO: transform src into the like-volume: orig.mgz changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram writing to orig_nu.mgz... Wed Aug 9 14:03:43 EDT 2017 mri_nu_correct.mni done talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri /home/lab/Desktop/freesurfer/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.8 2016/02/16 17:17:20 zkaufman Exp $ Linux lab-ThinkStation-E31 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux Wed Aug 9 14:03:43 EDT 2017 tmpdir is transforms/tmp.talairach.10626 /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri mri_convert orig_nu.mgz transforms/tmp.talairach.10626/src.mnc mri_convert.bin orig_nu.mgz transforms/tmp.talairach.10626/src.mnc $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig_nu.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to transforms/tmp.talairach.10626/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /home/lab/Desktop/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.10626/src.mnc transforms/talairach.auto.xfm Transforming slices:................................................................................................................................Done Copying chunks:......................................................................................................................................................Done. Copying chunks:..........................................................................................................Done. Transforming slices:......................................................................................................................................................Done Copying chunks:....................................................................................................................Done. Copying chunks:....................................................................................................................Done. Source volume size: 74 by 106 by 106 Source voxel size = 2.000 2.000 2.000 Source min/max real range = -0.000 237.238 Source min/max voxel= -0.000 237.238 Target volume size: 58 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.970 123.710 Target min/max voxel = -0.000 123.710 AFTER init_params() Transform matrix = 1.0000 0.0000 0.0000 -5.8189 0.0000 1.0000 0.0000 -18.1802 0.0000 0.0000 1.0000 -15.3079 Transform center = 6.147 0.589 24.762 Transform rotations = 0.000 0.000 0.000 Transform trans = -5.819 -18.180 -15.308 Transform scale = 1.000 1.000 1.000 Transform shear = 0.000 0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -85.095 -125.510 -47.250 Lattice count = 43 55 29 Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = -0.000 251.001 Source min/max voxel= -0.000 251.001 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= -0.000 144.070 Target min/max voxel = -0.000 144.070 AFTER init_params() Transform matrix = 0.4765 -0.8606 -0.8676 4.5402 1.1709 0.0549 0.5885 -41.1334 -0.3498 -0.9883 0.7882 -23.9790 Transform center = 6.147 0.589 24.762 Transform rotations = -0.898 0.270 1.184 Transform trans = -20.669 -19.920 -31.956 Transform scale = 1.312 1.312 1.312 Transform shear = 0.000 -0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -85.095 -125.510 -57.250 Lattice count = 43 55 34 Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.073 26.427 Source min/max voxel= 0.073 26.427 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652 AFTER init_params() Transform matrix = 0.5807 -0.7529 -0.9406 5.0771 1.1477 0.0280 0.6862 -43.4293 -0.3666 -1.1051 0.6582 -22.9359 Transform center = 6.147 0.589 24.762 Transform rotations = -1.034 0.278 1.102 Transform trans = -21.235 -19.955 -34.304 Transform scale = 1.337 1.337 1.337 Transform shear = 0.000 0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.073 26.427 Source min/max voxel= 0.073 26.427 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652 AFTER init_params() Transform matrix = 0.7072 -0.7870 -0.9036 1.0205 1.1067 0.0268 0.8429 -42.2400 -0.4594 -1.1471 0.6396 -27.3785 Transform center = 6.147 0.589 24.762 Transform rotations = -1.062 0.336 1.002 Transform trans = -23.618 -15.139 -39.802 Transform scale = 1.391 1.391 1.391 Transform shear = 0.000 0.000 -0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.073 26.427 Source min/max voxel= 0.073 26.427 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652 AFTER init_params() Transform matrix = 0.6297 -0.8238 -0.8386 -2.4854 1.0090 0.0791 0.6800 -45.8947 -0.3877 -1.0003 0.6916 -55.1225 Transform center = 6.147 0.589 24.762 Transform rotations = -0.966 0.309 1.052 Transform trans = -26.012 -23.398 -65.732 Transform scale = 1.334 1.219 1.276 Transform shear = -0.000 -0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 Source volume size: 84 by 116 by 116 Source voxel size = 2.000 2.000 2.000 Source min/max real range = 0.073 26.427 Source min/max voxel= 0.073 26.427 Target volume size: 68 by 110 by 86 Target voxel = 2.000 2.000 2.000 Target min/max real range= 0.037 11.652 Target min/max voxel = 0.037 11.652 AFTER init_params() Transform matrix = 0.4215 -0.1872 -1.2193 11.5017 1.1611 0.3447 0.3485 -41.5924 0.3258 -1.4339 0.3327 -28.9081 Transform center = 6.147 0.589 24.762 Transform rotations = -1.343 -0.218 1.233 Transform trans = -22.358 -26.212 -44.273 Transform scale = 1.304 1.260 1.508 Transform shear = 0.000 -0.000 0.000 Target volume is smallest Lattice step size = 4.000 4.000 4.000 Lattice start = -65.095 -105.510 -57.250 Lattice count = 35 46 34 Wed Aug 9 14:03:51 EDT 2017 talairach done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Wed Aug 9 14:03:53 EDT 2017 /home/lab/Desktop/freesurfer/subjects/sub-09-AW-error/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < 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 ERROR: Talairach failed! Linux lab-ThinkStation-E31 4.10.0-28-generic #32~16.04.2-Ubuntu SMP Thu Jul 20 10:19:48 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-09-AW-error exited with ERRORS at Wed Aug 9 14:03:54 EDT 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting