Wed Jul 26 13:48:09 EDT 2017 /shared_data2/sneha/MSKCC_Processed/ped1_base /usr/local/freesurfer/bin/recon-all -base ped1_base -tp ped1_0 -tp ped1_1 -tp ped1_2 -tp ped1_3 -tp ped1_4 -all subjid ped1_base setenv SUBJECTS_DIR /shared_data2/sneha/MSKCC_Processed FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux gizmo 4.4.0-78-generic #99-Ubuntu SMP Thu Apr 27 15:29:09 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 47474 maxlocks unlimited maxsignal 47474 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 12261076 4128296 849968 105148 7282812 7653796 Swap: 8292348 0 8292348 ######################################## 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: 2017/07/26-17:48:09-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-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: 2017/07/26-17:48:09-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-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: 2017/07/26-17:48:09-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:10-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:10-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:10-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:10-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:10-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:10-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:10-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:10-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:10-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:11-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:11-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:11-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:11-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:11-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:11-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:11-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:12-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:12-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:12-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:12-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:12-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:12-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:12-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:12-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:12-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:13-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:13-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:13-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:13-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-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: 2017/07/26-17:48:13-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-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: 2017/07/26-17:48:13-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:13-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:13-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:14-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2017/07/26-17:48:14-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: sneha Machine: gizmo Platform: Linux PlatformVersion: 4.4.0-78-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/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/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# Longitudinal Base Subject Creation Wed Jul 26 13:48:14 EDT 2017 /shared_data2/sneha/MSKCC_Processed/ped1_base mri_diff --notallow-pix /shared_data2/sneha/MSKCC_Processed/ped1_1/mri/rawavg.mgz /shared_data2/sneha/MSKCC_Processed/ped1_0/mri/rawavg.mgz Volumes differ in dimension v1dim 412 512 512 1 v2dim 124 512 512 1 mri_diff --notallow-pix /shared_data2/sneha/MSKCC_Processed/ped1_2/mri/rawavg.mgz /shared_data2/sneha/MSKCC_Processed/ped1_0/mri/rawavg.mgz Volumes differ in dimension v1dim 512 412 512 1 v2dim 124 512 512 1 mri_diff --notallow-pix /shared_data2/sneha/MSKCC_Processed/ped1_3/mri/rawavg.mgz /shared_data2/sneha/MSKCC_Processed/ped1_0/mri/rawavg.mgz Volumes differ in dimension v1dim 280 512 512 1 v2dim 124 512 512 1 mri_diff --notallow-pix /shared_data2/sneha/MSKCC_Processed/ped1_4/mri/rawavg.mgz /shared_data2/sneha/MSKCC_Processed/ped1_0/mri/rawavg.mgz Volumes differ in dimension v1dim 412 512 512 1 v2dim 124 512 512 1 ******************************************************************************* WARNING: Image geometries differ across time, maybe due to aquisition changes? This can potentially bias a longitudinal study! Will continue in 10s. ******************************************************************************* mri_robust_template --mov /shared_data2/sneha/MSKCC_Processed/ped1_0/mri/norm.mgz /shared_data2/sneha/MSKCC_Processed/ped1_1/mri/norm.mgz /shared_data2/sneha/MSKCC_Processed/ped1_2/mri/norm.mgz /shared_data2/sneha/MSKCC_Processed/ped1_3/mri/norm.mgz /shared_data2/sneha/MSKCC_Processed/ped1_4/mri/norm.mgz --lta /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/transforms/ped1_0_to_ped1_base.lta /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/transforms/ped1_1_to_ped1_base.lta /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/transforms/ped1_2_to_ped1_base.lta /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/transforms/ped1_3_to_ped1_base.lta /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/transforms/ped1_4_to_ped1_base.lta --template /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/norm_template.mgz --average 1 --sat 4.685 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ --mov: Using /shared_data2/sneha/MSKCC_Processed/ped1_0/mri/norm.mgz as movable/source volume. --mov: Using /shared_data2/sneha/MSKCC_Processed/ped1_1/mri/norm.mgz as movable/source volume. --mov: Using /shared_data2/sneha/MSKCC_Processed/ped1_2/mri/norm.mgz as movable/source volume. --mov: Using /shared_data2/sneha/MSKCC_Processed/ped1_3/mri/norm.mgz as movable/source volume. --mov: Using /shared_data2/sneha/MSKCC_Processed/ped1_4/mri/norm.mgz as movable/source volume. Total: 5 input volumes --lta: Will output LTA transforms --template: Using /shared_data2/sneha/MSKCC_Processed/ped1_base/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 '/shared_data2/sneha/MSKCC_Processed/ped1_0/mri/norm.mgz'... converting source '/shared_data2/sneha/MSKCC_Processed/ped1_0/mri/norm.mgz' to bspline ... MRItoBSpline degree 3 reading source '/shared_data2/sneha/MSKCC_Processed/ped1_1/mri/norm.mgz'... converting source '/shared_data2/sneha/MSKCC_Processed/ped1_1/mri/norm.mgz' to bspline ... MRItoBSpline degree 3 reading source '/shared_data2/sneha/MSKCC_Processed/ped1_2/mri/norm.mgz'... converting source '/shared_data2/sneha/MSKCC_Processed/ped1_2/mri/norm.mgz' to bspline ... MRItoBSpline degree 3 reading source '/shared_data2/sneha/MSKCC_Processed/ped1_3/mri/norm.mgz'... converting source '/shared_data2/sneha/MSKCC_Processed/ped1_3/mri/norm.mgz' to bspline ... MRItoBSpline degree 3 reading source '/shared_data2/sneha/MSKCC_Processed/ped1_4/mri/norm.mgz'... converting source '/shared_data2/sneha/MSKCC_Processed/ped1_4/mri/norm.mgz' to bspline ... MRItoBSpline degree 3 Will use TP 5 as random initial target (seed 32284 ). MultiRegistration::initializing Xforms (init 5 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 5 ============================== Register TP 2 ( /shared_data2/sneha/MSKCC_Processed/ped1_1/mri/norm.mgz ) to TP 5 ( /shared_data2/sneha/MSKCC_Processed/ped1_4/mri/norm.mgz ) [init] ========================= TP 3 to TP 5 ============================== Register TP 3 ( /shared_data2/sneha/MSKCC_Processed/ped1_2/mri/norm.mgz ) to TP 5 ( /shared_data2/sneha/MSKCC_Processed/ped1_4/mri/norm.mgz ) [init] ========================= TP 4 to TP 5 ============================== Register TP 4 ( /shared_data2/sneha/MSKCC_Processed/ped1_3/mri/norm.mgz ) to TP 5 ( /shared_data2/sneha/MSKCC_Processed/ped1_4/mri/norm.mgz ) [init] ========================= TP 1 to TP 5 ============================== Register TP 1 ( /shared_data2/sneha/MSKCC_Processed/ped1_0/mri/norm.mgz ) to TP 5 ( /shared_data2/sneha/MSKCC_Processed/ped1_4/mri/norm.mgz ) computing coord of TP 2 ( /shared_data2/sneha/MSKCC_Processed/ped1_1/mri/norm.mgz ) wrt to TP 5 ( /shared_data2/sneha/MSKCC_Processed/ped1_4/mri/norm.mgz ) computing coord of TP 3 ( /shared_data2/sneha/MSKCC_Processed/ped1_2/mri/norm.mgz ) wrt to TP 5 ( /shared_data2/sneha/MSKCC_Processed/ped1_4/mri/norm.mgz ) computing coord of TP 4 ( /shared_data2/sneha/MSKCC_Processed/ped1_3/mri/norm.mgz ) wrt to TP 5 ( /shared_data2/sneha/MSKCC_Processed/ped1_4/mri/norm.mgz ) computing coord of TP 1 ( /shared_data2/sneha/MSKCC_Processed/ped1_0/mri/norm.mgz ) wrt to TP 5 ( /shared_data2/sneha/MSKCC_Processed/ped1_4/mri/norm.mgz ) computing mean coord of TP 5 ( /shared_data2/sneha/MSKCC_Processed/ped1_4/mri/norm.mgz ) mapping back to rot, err = 7.10326e-08 computing mean coord of TP 2 ( /shared_data2/sneha/MSKCC_Processed/ped1_1/mri/norm.mgz ) mapping back to rot, err = 1.58584e-07 computing mean coord of TP 3 ( /shared_data2/sneha/MSKCC_Processed/ped1_2/mri/norm.mgz ) mapping back to rot, err = 1.18512e-07 computing mean coord of TP 4 ( /shared_data2/sneha/MSKCC_Processed/ped1_3/mri/norm.mgz ) mapping back to rot, err = 9.17618e-08 computing mean coord of TP 1 ( /shared_data2/sneha/MSKCC_Processed/ped1_0/mri/norm.mgz ) mapping back to rot, err = 9.03373e-08 Computing first template mapping movs and creating initial template... using median ======================================================= Working on global iteration : 1 ======================================================= noxformits = 3 Working on TP 1 - running multi-resolutional registration on TP 1... tp 1 distance: 0.0951979 - mapping tp 1 to template (cubic bspline) ... Finished TP : 1 ===================================================== Working on TP 2 - running multi-resolutional registration on TP 2... tp 2 distance: 0.077791 - mapping tp 2 to template (cubic bspline) ... Finished TP : 2 ===================================================== Working on TP 3 - running multi-resolutional registration on TP 3... tp 3 distance: 0.0738036 - mapping tp 3 to template (cubic bspline) ... Finished TP : 3 ===================================================== Working on TP 4 - running multi-resolutional registration on TP 4... tp 4 distance: 0.0989854 - mapping tp 4 to template (cubic bspline) ... Finished TP : 4 ===================================================== Working on TP 5 - running multi-resolutional registration on TP 5... tp 5 distance: 0.0520065 - mapping tp 5 to template (cubic bspline) ... Finished TP : 5 ===================================================== Global Iteration 1 Distances: 0.0951979 0.077791 0.0738036 0.0989854 0.0520065 Maxchange: 0.0989854 Computing new template 1 using median ======================================================= Working on global iteration : 2 ======================================================= noxformits = 1 Working on TP 1 - running multi-resolutional registration on TP 1... tp 1 distance: 0.0305687 - mapping tp 1 to template (cubic bspline) ... Finished TP : 1 ===================================================== Working on TP 2 - running multi-resolutional registration on TP 2... tp 2 distance: 0.0241491 - mapping tp 2 to template (cubic bspline) ... Finished TP : 2 ===================================================== Working on TP 3 - running multi-resolutional registration on TP 3... tp 3 distance: 0.0251975 - mapping tp 3 to template (cubic bspline) ... Finished TP : 3 ===================================================== Working on TP 4 - running multi-resolutional registration on TP 4... tp 4 distance: 0.0245003 - mapping tp 4 to template (cubic bspline) ... Finished TP : 4 ===================================================== Working on TP 5 - running multi-resolutional registration on TP 5... tp 5 distance: 0.0177901 - mapping tp 5 to template (cubic bspline) ... Finished TP : 5 ===================================================== Global Iteration 2 Distances: 0.0305687 0.0241491 0.0251975 0.0245003 0.0177901 Maxchange: 0.0305687 Computing new template 2 using median ======================================================= Working on global iteration : 3 ======================================================= Working on TP 1 - running multi-resolutional registration on TP 1... tp 1 distance: 0.0218774 - mapping tp 1 to template (cubic bspline) ... Finished TP : 1 ===================================================== Working on TP 2 - running multi-resolutional registration on TP 2... tp 2 distance: 0.021236 - mapping tp 2 to template (cubic bspline) ... Finished TP : 2 ===================================================== Working on TP 3 - running multi-resolutional registration on TP 3... tp 3 distance: 0.0213482 - mapping tp 3 to template (cubic bspline) ... Finished TP : 3 ===================================================== Working on TP 4 - running multi-resolutional registration on TP 4... tp 4 distance: 0.0207885 - mapping tp 4 to template (cubic bspline) ... Finished TP : 4 ===================================================== Working on TP 5 - running multi-resolutional registration on TP 5... tp 5 distance: 0.0200597 - mapping tp 5 to template (cubic bspline) ... Finished TP : 5 ===================================================== Global Iteration 3 Distances: 0.0218774 0.021236 0.0213482 0.0207885 0.0200597 Maxchange: 0.0218774 Computing new template 3 using median DONE : computeTemplate Writing final template: /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/norm_template.mgz Writing final transforms (warps etc.)... Determinant( lta[ 0 ]) : 1 Determinant( lta[ 1 ]) : 1 Determinant( lta[ 2 ]) : 1 Determinant( lta[ 3 ]) : 1 Determinant( lta[ 4 ]) : 1 registration took 14 minutes and 4 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 /shared_data2/sneha/MSKCC_Processed/ped1_0/mri/orig.mgz /shared_data2/sneha/MSKCC_Processed/ped1_1/mri/orig.mgz /shared_data2/sneha/MSKCC_Processed/ped1_2/mri/orig.mgz /shared_data2/sneha/MSKCC_Processed/ped1_3/mri/orig.mgz /shared_data2/sneha/MSKCC_Processed/ped1_4/mri/orig.mgz --average 1 --ixforms /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/transforms/ped1_0_to_ped1_base.lta /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/transforms/ped1_1_to_ped1_base.lta /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/transforms/ped1_2_to_ped1_base.lta /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/transforms/ped1_3_to_ped1_base.lta /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/transforms/ped1_4_to_ped1_base.lta --noit --template /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/orig.mgz $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ --mov: Using /shared_data2/sneha/MSKCC_Processed/ped1_0/mri/orig.mgz as movable/source volume. --mov: Using /shared_data2/sneha/MSKCC_Processed/ped1_1/mri/orig.mgz as movable/source volume. --mov: Using /shared_data2/sneha/MSKCC_Processed/ped1_2/mri/orig.mgz as movable/source volume. --mov: Using /shared_data2/sneha/MSKCC_Processed/ped1_3/mri/orig.mgz as movable/source volume. --mov: Using /shared_data2/sneha/MSKCC_Processed/ped1_4/mri/orig.mgz as movable/source volume. Total: 5 input volumes --average: Using method 1 for template computation. --ixforms: Will use init XFORMS. --noit: Will output only first template (no iterations)! --template: Using /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/orig.mgz as template output volume. reading source '/shared_data2/sneha/MSKCC_Processed/ped1_0/mri/orig.mgz'... converting source '/shared_data2/sneha/MSKCC_Processed/ped1_0/mri/orig.mgz' to bspline ... MRItoBSpline degree 3 reading source '/shared_data2/sneha/MSKCC_Processed/ped1_1/mri/orig.mgz'... converting source '/shared_data2/sneha/MSKCC_Processed/ped1_1/mri/orig.mgz' to bspline ... MRItoBSpline degree 3 reading source '/shared_data2/sneha/MSKCC_Processed/ped1_2/mri/orig.mgz'... converting source '/shared_data2/sneha/MSKCC_Processed/ped1_2/mri/orig.mgz' to bspline ... MRItoBSpline degree 3 reading source '/shared_data2/sneha/MSKCC_Processed/ped1_3/mri/orig.mgz'... converting source '/shared_data2/sneha/MSKCC_Processed/ped1_3/mri/orig.mgz' to bspline ... MRItoBSpline degree 3 reading source '/shared_data2/sneha/MSKCC_Processed/ped1_4/mri/orig.mgz'... converting source '/shared_data2/sneha/MSKCC_Processed/ped1_4/mri/orig.mgz' to bspline ... MRItoBSpline degree 3 mapping movs and creating initial template... using median Writing final template: /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/orig.mgz Writing final transforms (warps etc.)... registration took 0 minutes and 59 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 /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/transforms mri_concatenate_lta -invert1 ped1_0_to_ped1_base.lta identity.nofile ped1_base_to_ped1_0.lta invert the first LTA before applying it Read individual LTAs Writing LTA to file ped1_base_to_ped1_0.lta... mri_concatenate_lta successful. mri_concatenate_lta -invert1 ped1_1_to_ped1_base.lta identity.nofile ped1_base_to_ped1_1.lta invert the first LTA before applying it Read individual LTAs Writing LTA to file ped1_base_to_ped1_1.lta... mri_concatenate_lta successful. mri_concatenate_lta -invert1 ped1_2_to_ped1_base.lta identity.nofile ped1_base_to_ped1_2.lta invert the first LTA before applying it Read individual LTAs Writing LTA to file ped1_base_to_ped1_2.lta... mri_concatenate_lta successful. mri_concatenate_lta -invert1 ped1_3_to_ped1_base.lta identity.nofile ped1_base_to_ped1_3.lta invert the first LTA before applying it Read individual LTAs Writing LTA to file ped1_base_to_ped1_3.lta... mri_concatenate_lta successful. mri_concatenate_lta -invert1 ped1_4_to_ped1_base.lta identity.nofile ped1_base_to_ped1_4.lta invert the first LTA before applying it Read individual LTAs Writing LTA to file ped1_base_to_ped1_4.lta... mri_concatenate_lta successful. #-------------------------------------------- #@# MotionCor Wed Jul 26 14:04:13 EDT 2017 mri_add_xform_to_header -c /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/transforms/talairach.xfm /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/orig.mgz /shared_data2/sneha/MSKCC_Processed/ped1_base/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Wed Jul 26 14:04:14 EDT 2017 /shared_data2/sneha/MSKCC_Processed/ped1_base/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux gizmo 4.4.0-78-generic #99-Ubuntu SMP Thu Apr 27 15:29:09 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux recon-all -s ped1_base exited with ERRORS at Wed Jul 26 14:04:17 EDT 2017 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting