Mon Feb 8 13:34:27 UTC 2021 /execute/base_freesurfer /usr/local/freesurfer/bin/recon-all -base base_freesurfer -tp freesurfer -tp freesurfer_TS3 -all subjid base_freesurfer setenv SUBJECTS_DIR /execute FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux 92df0dd7a4e2 5.4.0-1030-aws #31~18.04.1-Ubuntu SMP Tue Nov 17 10:48:34 UTC 2020 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize unlimited memoryuse unlimited vmemoryuse unlimited descriptors 1048576 memorylocked 16384 kbytes maxproc unlimited maxlocks unlimited maxsignal 31330 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 8049168 644776 203552 944 7200840 7097976 Swap: 0 0 0 ######################################## 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: 2021/02/08-13:34:27-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws 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: 2021/02/08-13:34:27-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: N3 1.12.00 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/02/08-13:34:27-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/02/08-13:34:27-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/02/08-13:34:27-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws 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: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws 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: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2021/02/08-13:34:28-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: docker Machine: 92df0dd7a4e2 Platform: Linux PlatformVersion: 5.4.0-1030-aws CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/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 /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# Longitudinal Base Subject Creation Mon Feb 8 13:34:28 UTC 2021 /execute/base_freesurfer mri_diff --notallow-pix --notallow-geo /execute/freesurfer_TS3/mri/rawavg.mgz /execute/freesurfer/mri/rawavg.mgz mri_robust_template --mov /execute/freesurfer/mri/norm.mgz /execute/freesurfer_TS3/mri/norm.mgz --lta /execute/base_freesurfer/mri/transforms/freesurfer_to_base_freesurfer.lta /execute/base_freesurfer/mri/transforms/freesurfer_TS3_to_base_freesurfer.lta --template /execute/base_freesurfer/mri/norm_template.mgz --average 1 --sat 4.685 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ --mov: Using /execute/freesurfer/mri/norm.mgz as movable/source volume. --mov: Using /execute/freesurfer_TS3/mri/norm.mgz as movable/source volume. Total: 2 input volumes --lta: Will output LTA transforms --template: Using /execute/base_freesurfer/mri/norm_template.mgz as template output volume. --average: Using method 1 for template computation. --sat: Using saturation 4.685 in M-estimator! reading source '/execute/freesurfer/mri/norm.mgz'... converting source '/execute/freesurfer/mri/norm.mgz' to bspline ... MRItoBSpline degree 3 reading source '/execute/freesurfer_TS3/mri/norm.mgz'... converting source '/execute/freesurfer_TS3/mri/norm.mgz' to bspline ... MRItoBSpline degree 3 Will use TP 2 as random initial target (seed 11672 ). MultiRegistration::initializing Xforms (init 2 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 1 to TP 2 ============================== Register TP 1 ( /execute/freesurfer/mri/norm.mgz ) to TP 2 ( /execute/freesurfer_TS3/mri/norm.mgz ) Input rotation's max deviation from rotation is: 3.36851e-07 computing mean coord of TP 2 ( /execute/freesurfer_TS3/mri/norm.mgz ) mapping back to rot, err = 1.11022e-16 computing mean coord of TP 1 ( /execute/freesurfer/mri/norm.mgz ) mapping back to rot, err = 1.68426e-07 mapping movs and creating initial template... using median Writing final template: /execute/base_freesurfer/mri/norm_template.mgz Writing final transforms (warps etc.)... Determinant( lta[ 0 ]) : 1 Determinant( lta[ 1 ]) : 1 registration took 0 minutes and 43 seconds. Thank you for using RobustTemplate! If you find it useful and use it for a publication, please cite: Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis M. Reuter, N.J. Schmansky, H.D. Rosas, B. Fischl. NeuroImage 2012. http://dx.doi.org/10.1016/j.neuroimage.2012.02.084 http://reuter.mit.edu/papers/reuter-long12.pdf mri_robust_template --mov /execute/freesurfer/mri/orig.mgz /execute/freesurfer_TS3/mri/orig.mgz --average 1 --ixforms /execute/base_freesurfer/mri/transforms/freesurfer_to_base_freesurfer.lta /execute/base_freesurfer/mri/transforms/freesurfer_TS3_to_base_freesurfer.lta --noit --template /execute/base_freesurfer/mri/orig.mgz $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ --mov: Using /execute/freesurfer/mri/orig.mgz as movable/source volume. --mov: Using /execute/freesurfer_TS3/mri/orig.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --ixforms: Will use init XFORMS. --noit: Will output only first template (no iterations)! --template: Using /execute/base_freesurfer/mri/orig.mgz as template output volume. reading source '/execute/freesurfer/mri/orig.mgz'... converting source '/execute/freesurfer/mri/orig.mgz' to bspline ... MRItoBSpline degree 3 reading source '/execute/freesurfer_TS3/mri/orig.mgz'... converting source '/execute/freesurfer_TS3/mri/orig.mgz' to bspline ... MRItoBSpline degree 3 mapping movs and creating initial template... using median Writing final template: /execute/base_freesurfer/mri/orig.mgz Writing final transforms (warps etc.)... registration took 0 minutes and 19 seconds. Thank you for using RobustTemplate! If you find it useful and use it for a publication, please cite: Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis M. Reuter, N.J. Schmansky, H.D. Rosas, B. Fischl. NeuroImage 2012. http://dx.doi.org/10.1016/j.neuroimage.2012.02.084 http://reuter.mit.edu/papers/reuter-long12.pdf /execute/base_freesurfer/mri/transforms mri_concatenate_lta -invert1 freesurfer_to_base_freesurfer.lta identity.nofile base_freesurfer_to_freesurfer.lta invert the first LTA before applying it Read individual LTAs Writing LTA to file base_freesurfer_to_freesurfer.lta... mri_concatenate_lta.bin successful. mri_concatenate_lta -invert1 freesurfer_TS3_to_base_freesurfer.lta identity.nofile base_freesurfer_to_freesurfer_TS3.lta invert the first LTA before applying it Read individual LTAs Writing LTA to file base_freesurfer_to_freesurfer_TS3.lta... mri_concatenate_lta.bin successful. #-------------------------------------------- #@# MotionCor Mon Feb 8 13:35:32 UTC 2021 mri_add_xform_to_header -c /execute/base_freesurfer/mri/transforms/talairach.xfm /execute/base_freesurfer/mri/orig.mgz /execute/base_freesurfer/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Mon Feb 8 13:35:33 UTC 2021 /execute/base_freesurfer/mri mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 /execute/base_freesurfer/mri /usr/local/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 92df0dd7a4e2 5.4.0-1030-aws #31~18.04.1-Ubuntu SMP Tue Nov 17 10:48:34 UTC 2020 x86_64 GNU/Linux Mon Feb 8 13:35:33 UTC 2021 Program nu_correct, built from: N3 1.12.00 /usr/bin/bc tmpdir is ./tmp.mri_nu_correct.mni.534 /execute/base_freesurfer/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.534/nu0.mnc -odt float mri_convert.bin orig.mgz ./tmp.mri_nu_correct.mni.534/nu0.mnc -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from orig.mgz... TR=7.51, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -1.9063e-09, 6.93889e-18) j_ras = (-1.38778e-17, 4.19095e-09, -1) k_ras = (-1.9063e-09, 1, 4.19095e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.534/nu0.mnc... -------------------------------------------------------- Iteration 1 Mon Feb 8 13:35:35 UTC 2021 nu_correct -clobber ./tmp.mri_nu_correct.mni.534/nu0.mnc ./tmp.mri_nu_correct.mni.534/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.534/0/ -iterations 1000 -distance 50 [docker@92df0dd7a4e2:/execute/base_freesurfer/mri/] [2021-02-08 13:35:35] running: /opt/minc/1.9.16/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.534/0/ ./tmp.mri_nu_correct.mni.534/nu0.mnc ./tmp.mri_nu_correct.mni.534/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 36 CV of field change: 0.000980265 mri_convert ./tmp.mri_nu_correct.mni.534/nu1.mnc orig_nu.mgz --like orig.mgz --conform mri_convert.bin ./tmp.mri_nu_correct.mni.534/nu1.mnc orig_nu.mgz --like orig.mgz --conform ncopen: filename "./tmp.mri_nu_correct.mni.534/nu1.mnc": Not a netCDF file miopen: MINC package entry point Error opening ./tmp.mri_nu_correct.mni.534/nu1.mnc mincRead(): error reading volume from file ./tmp.mri_nu_correct.mni.534/nu1.mnc $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from ./tmp.mri_nu_correct.mni.534/nu1.mnc... Linux 92df0dd7a4e2 5.4.0-1030-aws #31~18.04.1-Ubuntu SMP Tue Nov 17 10:48:34 UTC 2020 x86_64 GNU/Linux recon-all -s base_freesurfer exited with ERRORS at Mon Feb 8 13:36:27 UTC 2021 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting