Fri Oct 30 18:42:28 CDT 2009 /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45 /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R450/bin/recon-all -base FREESURFERRECON_TEST_005_S_0221BASE45 -tp FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1 -tp FREESURFERRECON_TEST_005_S_0221v2_45_20061006.104318_1 -all -force subjid FREESURFERRECON_TEST_005_S_0221BASE45 setenv SUBJECTS_DIR /space/md8/6/data/TEST/FSContainers FREESURFER_HOME /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R450 Actual FREESURFER_HOME /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R450 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 Linux ip64.ucsd.edu 2.6.18-164.2.1.el5 #1 SMP Mon Sep 21 04:37:42 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 32 kbytes maxproc 407552 total used free shared buffers cached Mem: 49379092 7015284 42363808 0 200704 5402532 -/+ buffers/cache: 1412048 47967044 Swap: 14057464 0 14057464 ######################################## program versions used $Id: recon-all,v 1.133.2.57 2009/08/06 18:27:48 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.7.2.1 2008/02/29 20:17:11 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.4.2.1 2009/07/30 19:22:07 nicks Exp $ mri_convert --version stable4 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: tkregister2.c,v 1.86.2.12 2009/03/19 22:04:20 greve Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@kani (i686-pc-linux-gnu) on 2005-11-15 at 21:02:27 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_normalize.c,v 1.52.2.2 2008/05/12 17:34:55 nicks Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_watershed.cpp,v 1.67.2.5 2009/05/05 19:17:42 nicks Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_segment.c,v 1.33.2.2 2007/11/21 04:38:38 nicks Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_label2label.c,v 1.33 2007/08/10 18:23:46 greve Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_em_register.c,v 1.57.2.2 2008/12/29 17:22:03 nicks Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_ca_normalize.c,v 1.38.2.3 2009/08/02 15:00:46 nicks Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_ca_register.c,v 1.63.2.3 2009/07/30 22:39:45 nicks Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_ca_label.c,v 1.80.2.8 2009/07/30 23:22:53 nicks Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_pretess.c,v 1.16 2007/01/18 20:23:47 nicks Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 unknown option -ALL-INFO ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_fill.c,v 1.111 2007/07/19 20:16:38 fischl Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_concatenate_lta.c,v 1.3.2.1 2009/05/06 23:40:38 nicks Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_normalize_tp2.c,v 1.6 2007/01/08 18:10:12 nicks Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_smooth.c,v 1.21 2007/01/01 18:16:19 fischl Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_inflate.c,v 1.33.2.3 2008/04/22 19:47:47 nicks Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_curvature.c,v 1.25 2007/07/20 16:42:32 fischl Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_topo_fixer.cpp,v 1.26.2.1 2007/11/18 03:06:20 nicks Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10 nicks Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_make_surfaces.c,v 1.99.2.5 2008/08/21 22:48:22 nicks Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_register.c,v 1.48 2007/07/19 15:58:50 fischl Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_anatomical_stats.c,v 1.54.2.7 2009/06/08 23:45:06 nicks Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_curvature_stats.c,v 1.28.2.5 2009/02/04 21:12:59 nicks Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.22.2.1 2009/05/22 00:58:19 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_robust_register.cpp,v 1.22.2.1 2009/05/22 00:58:19 nicks Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.6.2.4 2009/08/05 16:30:00 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_robust_template.cpp,v 1.6.2.4 2009/08/05 16:30:00 nicks Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_and.c,v 1.2.2.1 2009/05/22 00:58:19 nicks Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_or.c,v 1.1.2.1 2009/06/09 19:52:43 nicks Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/10/30-23:42:28-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_fuse_segmentations.c,v 1.5.2.2 2009/06/10 19:42:00 nicks Exp $ User: dev Machine: ip64.ucsd.edu Platform: Linux PlatformVersion: 2.6.18-164.2.1.el5 CompilerName: GCC CompilerVersion: 30400 ####################################### GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs ####################################### #-------------------------------------------- #@# Longitudinal Base Subject Creation Fri Oct 30 18:42:28 CDT 2009 /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45 mri_robust_template --mov /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1/mri/norm.mgz /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221v2_45_20061006.104318_1/mri/norm.mgz --lta /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45/mri/transforms/FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1_to_FREESURFERRECON_TEST_005_S_0221BASE45.lta /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45/mri/transforms/FREESURFERRECON_TEST_005_S_0221v2_45_20061006.104318_1_to_FREESURFERRECON_TEST_005_S_0221BASE45.lta --average 1 --template /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45/mri/norm_template.mgz $Id: mri_robust_template.cpp,v 1.6.2.4 2009/08/05 16:30:00 nicks Exp $ Using /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1/mri/norm.mgz as movable/source volume. Using /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221v2_45_20061006.104318_1/mri/norm.mgz as movable/source volume. Using 2 input volumes Will output LTA transforms Using Method: 1 for template computation. Using /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45/mri/norm_template.mgz as template output volume. reading source '/space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1/mri/norm.mgz'... reading source '/space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221v2_45_20061006.104318_1/mri/norm.mgz'... Registration::computeMultiresRegistration - Gaussian Pyramid - computing initial Transform -- using translation info Resolution: 4 - compute new registration Iteration: 1 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.015625Mb mem for indexing ... done! -- compute derivatives ... done! -- size 12 12 12 ( 1679 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 5 ERR: 0.0239336 weights average: 0.728121 zero: 0.17468 DONE - store transform -- old difference to prev. transform: 0.126292 -- difference to prev. transform: 0.83584 Iteration: 2 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.015625Mb mem for indexing ... done! -- compute derivatives ... done! -- size 12 12 12 ( 1679 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 3 ERR: 0.0207 weights average: 0.712825 zero: 0.194529 DONE - store transform -- old difference to prev. transform: 0.120231 -- difference to prev. transform: 0.567453 Iteration: 3 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.015625Mb mem for indexing ... done! -- compute derivatives ... done! -- size 12 12 12 ( 1679 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 8 ERR: 0.0192928 weights average: 0.738045 zero: 0.17468 DONE - store transform -- old difference to prev. transform: 0.251137 -- difference to prev. transform: 1.16893 Iteration: 4 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.015625Mb mem for indexing ... done! -- compute derivatives ... done! -- size 12 12 12 ( 1679 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 9 ERR: 0.0232526 weights average: 0.749053 zero: 0.168485 DONE - store transform -- old difference to prev. transform: 0.00417552 -- difference to prev. transform: 0.180488 Iteration: 5 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.015625Mb mem for indexing ... done! -- compute derivatives ... done! -- size 12 12 12 ( 1679 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 5 ERR: 0.0206086 weights average: 0.744415 zero: 0.173019 DONE - store transform -- old difference to prev. transform: 0.0428461 -- difference to prev. transform: 0.200304 -- adjusting half-way maps Resolution: 3 - compute new registration Iteration: 1 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.125Mb mem for indexing ... done! -- compute derivatives ... done! -- size 28 28 28 ( 10357 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 6 ERR: 0.0604243 weights average: 0.692936 zero: 0.229934 DONE - store transform -- old difference to prev. transform: 0.173506 -- difference to prev. transform: 0.550598 Iteration: 2 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.125Mb mem for indexing ... done! -- compute derivatives ... done! -- size 28 28 28 ( 10346 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 6 ERR: 0.0566512 weights average: 0.685067 zero: 0.236562 DONE - store transform -- old difference to prev. transform: 0.0194672 -- difference to prev. transform: 0.167363 Iteration: 3 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.125Mb mem for indexing ... done! -- compute derivatives ... done! -- size 28 28 28 ( 10346 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 2 ERR: 0.0564972 weights average: 0.684801 zero: 0.23736 DONE - store transform -- old difference to prev. transform: 0.00788576 -- difference to prev. transform: 0.0304684 Iteration: 4 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.125Mb mem for indexing ... done! -- compute derivatives ... done! -- size 28 28 28 ( 10346 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 4 ERR: 0.0560544 weights average: 0.684513 zero: 0.237909 DONE - store transform -- old difference to prev. transform: 0.0186914 -- difference to prev. transform: 0.0742902 Iteration: 5 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.125Mb mem for indexing ... done! -- compute derivatives ... done! -- size 28 28 28 ( 10345 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 2 ERR: 0.0560693 weights average: 0.684173 zero: 0.237799 DONE - store transform -- old difference to prev. transform: 0.00468304 -- difference to prev. transform: 0.0202839 -- adjusting half-way maps Resolution: 2 - compute new registration Iteration: 1 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 1Mb mem for indexing ... done! -- compute derivatives ... done! -- size 60 60 60 ( 50785 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 3 ERR: 1.5809 weights average: 0.830497 zero: 0.0666454 DONE - store transform -- old difference to prev. transform: 0.389768 -- difference to prev. transform: 0.670898 Iteration: 2 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 1Mb mem for indexing ... done! -- compute derivatives ... done! -- size 60 60 60 ( 50508 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 2 ERR: 1.65471 weights average: 0.836142 zero: 0.0598491 DONE - store transform -- old difference to prev. transform: 0.0778559 -- difference to prev. transform: 0.137124 Iteration: 3 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 1Mb mem for indexing ... done! -- compute derivatives ... done! -- size 60 60 60 ( 50434 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 2 ERR: 1.67827 weights average: 0.839258 zero: 0.0563171 DONE - store transform -- old difference to prev. transform: 0.0498046 -- difference to prev. transform: 0.0856238 Iteration: 4 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 1Mb mem for indexing ... done! -- compute derivatives ... done! -- size 60 60 60 ( 50393 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 2 ERR: 1.72244 weights average: 0.843186 zero: 0.0533483 DONE - store transform -- old difference to prev. transform: 0.0341878 -- difference to prev. transform: 0.0575915 Iteration: 5 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 1Mb mem for indexing ... done! -- compute derivatives ... done! -- size 60 60 60 ( 50369 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 2 ERR: 1.75272 weights average: 0.845782 zero: 0.0509811 DONE - store transform -- old difference to prev. transform: 0.0233411 -- difference to prev. transform: 0.0400766 -- adjusting half-way maps Resolution: 1 - compute new registration Iteration: 1 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 8Mb mem for indexing ... done! -- compute derivatives ... done! -- size 124 124 124 ( 297476 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 3 ERR: 7.1209 weights average: 0.906372 zero: 0.0173584 DONE - store transform -- old difference to prev. transform: 0.247125 -- difference to prev. transform: 0.310918 Iteration: 2 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 8Mb mem for indexing ... done! -- compute derivatives ... done! -- size 124 124 124 ( 297079 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 2 ERR: 7.18039 weights average: 0.907158 zero: 0.0165208 DONE - store transform -- old difference to prev. transform: 0.0224921 -- difference to prev. transform: 0.0292248 Iteration: 3 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 8Mb mem for indexing ... done! -- compute derivatives ... done! -- size 124 124 124 ( 297040 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 2 ERR: 7.20834 weights average: 0.907636 zero: 0.0160429 DONE - store transform -- old difference to prev. transform: 0.0075421 -- difference to prev. transform: 0.00961421 Resolution: 0 - compute new registration Iteration: 1 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 64Mb mem for indexing ... done! -- compute derivatives ... done! -- size 252 252 252 ( 2085410 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 2 ERR: 12.8012 weights average: 0.918625 zero: 0.0129914 DONE - store transform -- old difference to prev. transform: 0.0573751 -- difference to prev. transform: 0.0603048 Iteration: 2 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 64Mb mem for indexing ... done! -- compute derivatives ... done! -- size 252 252 252 ( 2085248 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 2 ERR: 12.8671 weights average: 0.919322 zero: 0.0124257 DONE - store transform -- old difference to prev. transform: 0.0179104 -- difference to prev. transform: 0.0188112 Iteration: 3 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 64Mb mem for indexing ... done! -- compute derivatives ... done! -- size 252 252 252 ( 2085151 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 2 ERR: 12.9033 weights average: 0.919611 zero: 0.0122047 DONE - store transform -- old difference to prev. transform: 0.00575266 -- difference to prev. transform: 0.00615682 creating half way data ... creating half-way template ... applying the vox to vox linear transform 1.000 -0.003 0.003 0.044; 0.003 1.000 -0.001 -0.300; -0.003 0.001 1.000 0.100; 0.000 0.000 0.000 1.000; applying the vox to vox linear transform 1.000 0.003 -0.003 -0.043; -0.003 1.000 0.001 0.300; 0.003 -0.001 1.000 -0.100; 0.000 0.000 0.000 1.000; using median Writing final template: /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45/mri/norm_template.mgz Writing final transforms (warps etc.)... registration took 3 minutes and 37 seconds. mri_robust_template --mov /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1/mri/orig.mgz /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221v2_45_20061006.104318_1/mri/orig.mgz --average 1 --ixforms /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45/mri/transforms/FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1_to_FREESURFERRECON_TEST_005_S_0221BASE45.lta /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45/mri/transforms/FREESURFERRECON_TEST_005_S_0221v2_45_20061006.104318_1_to_FREESURFERRECON_TEST_005_S_0221BASE45.lta --noit --template /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45/mri/orig/001.mgz $Id: mri_robust_template.cpp,v 1.6.2.4 2009/08/05 16:30:00 nicks Exp $ Using /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1/mri/orig.mgz as movable/source volume. Using /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221v2_45_20061006.104318_1/mri/orig.mgz as movable/source volume. Using 2 input volumes Using Method: 1 for template computation. Will use init XFORMS. Will output only first template (no iterations)! Using /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45/mri/orig/001.mgz as template output volume. reading source '/space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1/mri/orig.mgz'... reading source '/space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221v2_45_20061006.104318_1/mri/orig.mgz'... Computing first template warping movs and creating template... using median Writing final template: /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45/mri/orig/001.mgz Writing final transforms (warps etc.)... registration took 0 minutes and 9 seconds. /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45/mri/transforms mri_concatenate_lta -invert1 FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1_to_FREESURFERRECON_TEST_005_S_0221BASE45.lta identity.nofile FREESURFERRECON_TEST_005_S_0221BASE45_to_FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1.lta invert the first LTA before applying it MatrixInverse: NULL input matrix! Read individual LTAs Linux ip64.ucsd.edu 2.6.18-164.2.1.el5 #1 SMP Mon Sep 21 04:37:42 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Oct 30 18:46:14 CDT 2009 New invocation of recon-all Fri Oct 30 18:57:53 PDT 2009 /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45 /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R450/bin/recon-all -base FREESURFERRECON_TEST_005_S_0221BASE45 -tp FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1 -tp FREESURFERRECON_TEST_005_S_0221v2_45_20061006.104318_1 -all -force subjid FREESURFERRECON_TEST_005_S_0221BASE45 setenv SUBJECTS_DIR /space/md8/6/data/TEST/FSContainers FREESURFER_HOME /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R450 Actual FREESURFER_HOME /space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R450 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 Linux ip96.ucsd.edu 2.6.9-55.0.2.ELsmp #1 SMP Tue Jun 12 17:58:20 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 32 kbytes maxproc 73216 total used free shared buffers cached Mem: 7898364 6917428 980936 0 63304 5212436 -/+ buffers/cache: 1641688 6256676 Swap: 2040212 3644 2036568 ######################################## program versions used $Id: recon-all,v 1.133.2.57 2009/08/06 18:27:48 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.7.2.1 2008/02/29 20:17:11 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.4.2.1 2009/07/30 19:22:07 nicks Exp $ mri_convert --version stable4 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: tkregister2.c,v 1.86.2.12 2009/03/19 22:04:20 greve Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2005-11-15 at 20:37:35 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_normalize.c,v 1.52.2.2 2008/05/12 17:34:55 nicks Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_watershed.cpp,v 1.67.2.5 2009/05/05 19:17:42 nicks Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:54-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_segment.c,v 1.33.2.2 2007/11/21 04:38:38 nicks Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:55-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_label2label.c,v 1.33 2007/08/10 18:23:46 greve Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:55-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_em_register.c,v 1.57.2.2 2008/12/29 17:22:03 nicks Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:55-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_ca_normalize.c,v 1.38.2.3 2009/08/02 15:00:46 nicks Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:55-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_ca_register.c,v 1.63.2.3 2009/07/30 22:39:45 nicks Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:55-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_ca_label.c,v 1.80.2.8 2009/07/30 23:22:53 nicks Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:55-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_pretess.c,v 1.16 2007/01/18 20:23:47 nicks Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 unknown option -ALL-INFO ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:55-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_fill.c,v 1.111 2007/07/19 20:16:38 fischl Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:55-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_tessellate.c,v 1.32 2007/04/26 21:44:21 fischl Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:55-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_concatenate_lta.c,v 1.3.2.1 2009/05/06 23:40:38 nicks Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:55-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_normalize_tp2.c,v 1.6 2007/01/08 18:10:12 nicks Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:56-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_smooth.c,v 1.21 2007/01/01 18:16:19 fischl Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:56-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_inflate.c,v 1.33.2.3 2008/04/22 19:47:47 nicks Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:56-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_curvature.c,v 1.25 2007/07/20 16:42:32 fischl Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:56-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:56-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:56-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_topo_fixer.cpp,v 1.26.2.1 2007/11/18 03:06:20 nicks Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:56-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_ca_label.c,v 1.23 2007/03/23 20:00:07 fischl Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:56-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_euler_number.c,v 1.5 2006/12/29 02:09:10 nicks Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:56-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_make_surfaces.c,v 1.99.2.5 2008/08/21 22:48:22 nicks Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:57-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_register.c,v 1.48 2007/07/19 15:58:50 fischl Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:57-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_anatomical_stats.c,v 1.54.2.7 2009/06/08 23:45:06 nicks Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:57-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mrisp_paint.c,v 1.8 2007/02/13 16:57:23 fischl Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:57-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mris_curvature_stats.c,v 1.28.2.5 2009/02/04 21:12:59 nicks Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.22.2.1 2009/05/22 00:58:19 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:57-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_robust_register.cpp,v 1.22.2.1 2009/05/22 00:58:19 nicks Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.6.2.4 2009/08/05 16:30:00 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:57-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_robust_template.cpp,v 1.6.2.4 2009/08/05 16:30:00 nicks Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2009/10/31-01:57:57-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_and.c,v 1.2.2.1 2009/05/22 00:58:19 nicks Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/10/31-01:57:57-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_or.c,v 1.1.2.1 2009/06/09 19:52:43 nicks Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2009/10/31-01:57:57-GMT BuildTimeStamp: Aug 11 2009 07:36:05 CVS: $Id: mri_fuse_segmentations.c,v 1.5.2.2 2009/06/10 19:42:00 nicks Exp $ User: dev Machine: ip96.ucsd.edu Platform: Linux PlatformVersion: 2.6.9-55.0.2.ELsmp CompilerName: GCC CompilerVersion: 30400 ####################################### GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCS curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs ####################################### #-------------------------------------------- #@# Longitudinal Base Subject Creation Fri Oct 30 18:57:57 PDT 2009 /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45 mri_robust_template --mov /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1/mri/norm.mgz /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221v2_45_20061006.104318_1/mri/norm.mgz --lta /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45/mri/transforms/FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1_to_FREESURFERRECON_TEST_005_S_0221BASE45.lta /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45/mri/transforms/FREESURFERRECON_TEST_005_S_0221v2_45_20061006.104318_1_to_FREESURFERRECON_TEST_005_S_0221BASE45.lta --average 1 --template /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45/mri/norm_template.mgz $Id: mri_robust_template.cpp,v 1.6.2.4 2009/08/05 16:30:00 nicks Exp $ Using /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1/mri/norm.mgz as movable/source volume. Using /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221v2_45_20061006.104318_1/mri/norm.mgz as movable/source volume. Using 2 input volumes Will output LTA transforms Using Method: 1 for template computation. Using /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45/mri/norm_template.mgz as template output volume. reading source '/space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1/mri/norm.mgz'... reading source '/space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221v2_45_20061006.104318_1/mri/norm.mgz'... Registration::computeMultiresRegistration - Gaussian Pyramid - computing initial Transform -- using translation info Resolution: 4 - compute new registration Iteration: 1 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.015625Mb mem for indexing ... done! -- compute derivatives ... done! -- size 12 12 12 ( 1679 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 5 ERR: 0.0239336 weights average: 0.728121 zero: 0.17468 DONE - store transform -- old difference to prev. transform: 0.126292 -- difference to prev. transform: 0.83584 Iteration: 2 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.015625Mb mem for indexing ... done! -- compute derivatives ... done! -- size 12 12 12 ( 1679 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 3 ERR: 0.0207 weights average: 0.712825 zero: 0.194529 DONE - store transform -- old difference to prev. transform: 0.120231 -- difference to prev. transform: 0.567453 Iteration: 3 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.015625Mb mem for indexing ... done! -- compute derivatives ... done! -- size 12 12 12 ( 1679 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 8 ERR: 0.0192928 weights average: 0.738045 zero: 0.17468 DONE - store transform -- old difference to prev. transform: 0.251137 -- difference to prev. transform: 1.16893 Iteration: 4 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.015625Mb mem for indexing ... done! -- compute derivatives ... done! -- size 12 12 12 ( 1679 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 9 ERR: 0.0232526 weights average: 0.749053 zero: 0.168485 DONE - store transform -- old difference to prev. transform: 0.00417552 -- difference to prev. transform: 0.180488 Iteration: 5 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.015625Mb mem for indexing ... done! -- compute derivatives ... done! -- size 12 12 12 ( 1679 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 5 ERR: 0.0206086 weights average: 0.744415 zero: 0.173019 DONE - store transform -- old difference to prev. transform: 0.0428461 -- difference to prev. transform: 0.200304 -- adjusting half-way maps Resolution: 3 - compute new registration Iteration: 1 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.125Mb mem for indexing ... done! -- compute derivatives ... done! -- size 28 28 28 ( 10357 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 6 ERR: 0.0604243 weights average: 0.692936 zero: 0.229934 DONE - store transform -- old difference to prev. transform: 0.173506 -- difference to prev. transform: 0.550598 Iteration: 2 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.125Mb mem for indexing ... done! -- compute derivatives ... done! -- size 28 28 28 ( 10346 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 6 ERR: 0.0566512 weights average: 0.685067 zero: 0.236562 DONE - store transform -- old difference to prev. transform: 0.0194672 -- difference to prev. transform: 0.167363 Iteration: 3 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.125Mb mem for indexing ... done! -- compute derivatives ... done! -- size 28 28 28 ( 10346 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 2 ERR: 0.0564972 weights average: 0.684801 zero: 0.23736 DONE - store transform -- old difference to prev. transform: 0.00788576 -- difference to prev. transform: 0.0304684 Iteration: 4 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.125Mb mem for indexing ... done! -- compute derivatives ... done! -- size 28 28 28 ( 10346 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 4 ERR: 0.0560544 weights average: 0.684513 zero: 0.237909 DONE - store transform -- old difference to prev. transform: 0.0186914 -- difference to prev. transform: 0.0742902 Iteration: 5 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 0.125Mb mem for indexing ... done! -- compute derivatives ... done! -- size 28 28 28 ( 10345 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 2 ERR: 0.0560693 weights average: 0.684173 zero: 0.237799 DONE - store transform -- old difference to prev. transform: 0.00468304 -- difference to prev. transform: 0.0202839 -- adjusting half-way maps Resolution: 2 - compute new registration Iteration: 1 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 1Mb mem for indexing ... done! -- compute derivatives ... done! -- size 60 60 60 ( 50785 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 3 ERR: 1.5809 weights average: 0.830497 zero: 0.0666454 DONE - store transform -- old difference to prev. transform: 0.389768 -- difference to prev. transform: 0.670898 Iteration: 2 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 1Mb mem for indexing ... done! -- compute derivatives ... done! -- size 60 60 60 ( 50508 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 2 ERR: 1.65471 weights average: 0.836142 zero: 0.0598491 DONE - store transform -- old difference to prev. transform: 0.0778559 -- difference to prev. transform: 0.137124 Iteration: 3 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 1Mb mem for indexing ... done! -- compute derivatives ... done! -- size 60 60 60 ( 50434 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 2 ERR: 1.67827 weights average: 0.839258 zero: 0.0563171 DONE - store transform -- old difference to prev. transform: 0.0498046 -- difference to prev. transform: 0.0856238 Iteration: 4 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 1Mb mem for indexing ... done! -- compute derivatives ... done! -- size 60 60 60 ( 50393 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 2 ERR: 1.72244 weights average: 0.843186 zero: 0.0533483 DONE - store transform -- old difference to prev. transform: 0.0341878 -- difference to prev. transform: 0.0575915 Iteration: 5 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 1Mb mem for indexing ... done! -- compute derivatives ... done! -- size 60 60 60 ( 50369 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 2 ERR: 1.75272 weights average: 0.845782 zero: 0.0509811 DONE - store transform -- old difference to prev. transform: 0.0233411 -- difference to prev. transform: 0.0400766 -- adjusting half-way maps Resolution: 1 - compute new registration Iteration: 1 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 8Mb mem for indexing ... done! -- compute derivatives ... done! -- size 124 124 124 ( 297476 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 3 ERR: 7.1209 weights average: 0.906372 zero: 0.0173584 DONE - store transform -- old difference to prev. transform: 0.247125 -- difference to prev. transform: 0.310918 Iteration: 2 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 8Mb mem for indexing ... done! -- compute derivatives ... done! -- size 124 124 124 ( 297079 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 2 ERR: 7.18039 weights average: 0.907158 zero: 0.0165208 DONE - store transform -- old difference to prev. transform: 0.0224921 -- difference to prev. transform: 0.0292248 Iteration: 3 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 8Mb mem for indexing ... done! -- compute derivatives ... done! -- size 124 124 124 ( 297040 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 2 ERR: 7.20834 weights average: 0.907636 zero: 0.0160429 DONE - store transform -- old difference to prev. transform: 0.0075421 -- difference to prev. transform: 0.00961421 Resolution: 0 - compute new registration Iteration: 1 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 64Mb mem for indexing ... done! -- compute derivatives ... done! -- size 252 252 252 ( 2085410 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 2 ERR: 12.8012 weights average: 0.918625 zero: 0.0129914 DONE - store transform -- old difference to prev. transform: 0.0573751 -- difference to prev. transform: 0.0603048 Iteration: 2 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 64Mb mem for indexing ... done! -- compute derivatives ... done! -- size 252 252 252 ( 2085248 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 2 ERR: 12.8671 weights average: 0.919322 zero: 0.0124257 DONE - store transform -- old difference to prev. transform: 0.0179104 -- difference to prev. transform: 0.0188112 Iteration: 3 - warping source and target (sqrt) - compute new registration - constructAb: -- allocating 64Mb mem for indexing ... done! -- compute derivatives ... done! -- size 252 252 252 ( 2085151 non-zero voxels ) - compute robust estimate ( sat 4.685 )... Step: 2 ERR: 12.9033 weights average: 0.919611 zero: 0.0122047 DONE - store transform -- old difference to prev. transform: 0.00575266 -- difference to prev. transform: 0.00615682 creating half way data ... creating half-way template ... applying the vox to vox linear transform 1.000 -0.003 0.003 0.044; 0.003 1.000 -0.001 -0.300; -0.003 0.001 1.000 0.100; 0.000 0.000 0.000 1.000; applying the vox to vox linear transform 1.000 0.003 -0.003 -0.043; -0.003 1.000 0.001 0.300; 0.003 -0.001 1.000 -0.100; 0.000 0.000 0.000 1.000; using median Writing final template: /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45/mri/norm_template.mgz Writing final transforms (warps etc.)... registration took 5 minutes and 54 seconds. mri_robust_template --mov /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1/mri/orig.mgz /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221v2_45_20061006.104318_1/mri/orig.mgz --average 1 --ixforms /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45/mri/transforms/FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1_to_FREESURFERRECON_TEST_005_S_0221BASE45.lta /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45/mri/transforms/FREESURFERRECON_TEST_005_S_0221v2_45_20061006.104318_1_to_FREESURFERRECON_TEST_005_S_0221BASE45.lta --noit --template /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45/mri/orig/001.mgz $Id: mri_robust_template.cpp,v 1.6.2.4 2009/08/05 16:30:00 nicks Exp $ Using /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1/mri/orig.mgz as movable/source volume. Using /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221v2_45_20061006.104318_1/mri/orig.mgz as movable/source volume. Using 2 input volumes Using Method: 1 for template computation. Will use init XFORMS. Will output only first template (no iterations)! Using /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45/mri/orig/001.mgz as template output volume. reading source '/space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1/mri/orig.mgz'... reading source '/space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221v2_45_20061006.104318_1/mri/orig.mgz'... Computing first template warping movs and creating template... using median Writing final template: /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45/mri/orig/001.mgz Writing final transforms (warps etc.)... registration took 0 minutes and 12 seconds. /space/md8/6/data/TEST/FSContainers/FREESURFERRECON_TEST_005_S_0221BASE45/mri/transforms mri_concatenate_lta -invert1 FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1_to_FREESURFERRECON_TEST_005_S_0221BASE45.lta identity.nofile FREESURFERRECON_TEST_005_S_0221BASE45_to_FREESURFERRECON_TEST_005_S_0221_45_20070321.105506_1.lta invert the first LTA before applying it MatrixInverse: NULL input matrix! Read individual LTAs Linux ip96.ucsd.edu 2.6.9-55.0.2.ELsmp #1 SMP Tue Jun 12 17:58:20 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Oct 30 19:04:03 PDT 2009