Hi Guang,
the registration fails, for example, if the RAS coordinates are stored incorrectly in the images (e.g. center outside the head). There is a new version of mri_robust_template, that uses moments instead of RAS coordinates for initial alignment. Download it here and rerun the base: http://reuter.mit.edu/index.php/software/robust/ replace it (and probably also mri_robust_register) in your freeSurfer and try again. Let me know if you still get errors.
Oh, you also need to specify --sat 4.685 in the first mri_robust_template call (search for it in recon-all script and add that parameter): set cmd = (mri_robust_template --mov ${normInVols}) set cmd = ($cmd --lta ${ltaXforms}) set cmd = ($cmd --average ${robust_template_avg_arg}) set cmd = ($cmd --template ${subjdir}/mri/norm_template.mgz) set cmd = ($cmd --sat 4.685 )
Also add that to mri_robust_register if you use the new version (in the long run): set cmd=(mri_robust_register) set cmd=($cmd --mov ${SUBJECTS_DIR}/${s}/mri/norm.mgz) set cmd=($cmd --dst ${subjdir}/mri/norm.mgz) set cmd=($cmd --lta ${subjdir}/mri/transforms/${s}_to_ ${subjid}.lta) set cmd=($cmd --sat 4.685 )
Best, Martin
On Mon, 2010-06-21 at 11:50 -0500, Guang Zeng wrote:
Hello, there,
I am running the FreeSurfer Longitudinal stream at the recon-all -base step. Both of the time points were successfully processed, and the recon-all -base process failed at the first step (robust registration).
I pasted the recon-all file below, can anyone help me to solve this problem?
Thanks! Guang
Mon Jun 21 11:23:53 CDT 2010 /data1/radiology/m047599/test3T_GW_New/018_S_0425_base /usr/local/biotools/freesurfer/freesurfer-v4.5.0/bin/recon-all -base 018_S_0425_base -tp 018_S_0425_20060619_160021_501 -tp 018_S_0425_20070615_092113_401 -all -force -notal-check -no-isrunning subjid 018_S_0425_base setenv SUBJECTS_DIR /data1/radiology/m047599/test3T_GW_New FREESURFER_HOME /usr/local/biotools/freesurfer/freesurfer-v4.5.0 Actual FREESURFER_HOME /home/biotools/freesurfer/freesurfer-v4.5.0 build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 Linux dnode49.mayo.edu 2.6.18-92.1.6.el5 #1 SMP Wed Jun 25 13:45:47 EDT 2008 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 135168
total used free shared bufferscached Mem: 16508820 8186556 8322264 0 121040 6433072 -/+ buffers/cache: 1632444 14876376 Swap: 33554424 10532 33543892
######################################## 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: 2010/06/21-16:23:53-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.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: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 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: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 unknown option -ALL-INFO ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.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: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.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: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/06/21-16:23:54-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: m047599 Machine: dnode49.mayo.edu Platform: Linux PlatformVersion: 2.6.18-92.1.6.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 Mon Jun 21 11:23:54 CDT 2010 /data1/radiology/m047599/test3T_GW_New/018_S_0425_base
mri_robust_template --mov /data1/radiology/m047599/test3T_GW_New/018_S_0425_20060619_160021_501/mri/norm.mgz /data1/radiology/m047599/test3T_GW_New/018_S_0425_20070615_092113_401/mri/norm.mgz --lta /data1/radiology/m047599/test3T_GW_New/018_S_0425_base/mri/transforms/018_S_0425_20060619_160021_501_to_018_S_0425_base.lta /data1/radiology/m047599/test3T_GW_New/018_S_0425_base/mri/transforms/018_S_0425_20070615_092113_401_to_018_S_0425_base.lta --average 1 --template /data1/radiology/m047599/test3T_GW_New/018_S_0425_base/mri/norm_template.mgz
$Id: mri_robust_template.cpp,v 1.6.2.4 2009/08/05 16:30:00 nicks Exp $ Using /data1/radiology/m047599/test3T_GW_New/018_S_0425_20060619_160021_501/mri/norm.mgz as movable/source volume. Using /data1/radiology/m047599/test3T_GW_New/018_S_0425_20070615_092113_401/mri/norm.mgz as movable/source volume. Using 2 input volumes Will output LTA transforms Using Method: 1 for template computation. Using /data1/radiology/m047599/test3T_GW_New/018_S_0425_base/mri/norm_template.mgz as template output volume. reading source '/data1/radiology/m047599/test3T_GW_New/018_S_0425_20060619_160021_501/mri/norm.mgz'... reading source '/data1/radiology/m047599/test3T_GW_New/018_S_0425_20070615_092113_401/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 ( 1685 non-zero voxels )
- compute robust estimate ( sat 4.685 )... Step: 12 ERR:
2.91623 weights average: 0.673008 zero: 0.272404 DONE
- store transform -- old difference to prev. transform: 12.997 -- difference to prev. transform: 57.8691
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 ( 1705 non-zero voxels )
- compute robust estimate ( sat 4.685 )... Step: 6 ERR: 8.27977 weights average: 0.668251 zero: 0.263652 DONE
- store transform -- old difference to prev. transform: 13.4697 -- difference to prev. transform: 53.1056
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 ( 1600 non-zero voxels )
- compute robust estimate ( sat 4.685 )... Step: 7 ERR: 12.9077 weights average: 0.68647 zero: 0.248436 DONE
- store transform -- old difference to prev. transform: 12.7052 -- difference to prev. transform: 47.541
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 ( 1365 non-zero voxels )
- compute robust estimate ( sat 4.685 )... Step: 3 ERR: 1.00415 weights average: 0.658358 zero: 0.304029 DONE
- store transform -- old difference to prev. transform: 6.53516 -- difference to prev. transform: 16.4189
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 ( 1081 non-zero voxels )
- compute robust estimate ( sat 4.685 )... Step: 3 ERR:
0.035687 weights average: 0.650796 zero: 0.321924 DONE
- store transform -- old difference to prev. transform: 3.90493 -- difference to prev. transform: 10.8376 -- 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 ( 5314 non-zero voxels )
- compute robust estimate ( sat 4.685 )... Step: 3 ERR: 0.24948 weights average: 0.611185 zero: 0.359616 DONE
- store transform -- old difference to prev. transform: 4.28862 -- difference to prev. transform: 6.43719
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 ( 4294 non-zero voxels )
- compute robust estimate ( sat 4.685 )... Step: 8 ERR:
0.160071 weights average: 0.617197 zero: 0.352352 DONE
- store transform -- old difference to prev. transform: 5.31445 -- difference to prev. transform: 9.87267
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 ( 3378 non-zero voxels )
- compute robust estimate ( sat 4.685 )... Step: 7 ERR:
0.0633697 weights average: 0.604518 zero: 0.37093 DONE
- store transform -- old difference to prev. transform: 4.12915 -- difference to prev. transform: 7.37041
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 ( 2632 non-zero voxels )
- compute robust estimate ( sat 4.685 )... Step: 3 ERR:
0.0562761 weights average: 0.605816 zero: 0.368541 DONE
- store transform -- old difference to prev. transform: 4.26114 -- difference to prev. transform: 8.22338
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 ( 2025 non-zero voxels )
- compute robust estimate ( sat 4.685 )... Step: 3 ERR:
0.059443 weights average: 0.609209 zero: 0.364938 DONE
- store transform -- old difference to prev. transform: 2.4914 -- difference to prev. transform: 7.55182 -- 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 ( 9552 non-zero voxels )
- compute robust estimate ( sat 4.685 )... Step: 3 ERR: 20.1679 weights average: 0.645418 zero: 0.305381 DONE
- store transform -- old difference to prev. transform: 8.52965 -- difference to prev. transform: 13.3328
Iteration: 2
- warping source and target (sqrt)
- compute new registration
- constructAb: -- allocating 1Mb mem for indexing ... done! -- compute derivatives ... done! -- size 60 60 60 ( 8126 non-zero voxels )
- compute robust estimate ( sat 4.685 )... Step: 3 ERR: 16.9521 weights average: 0.639884 zero: 0.314177 DONE
- store transform -- old difference to prev. transform: 7.61084 -- difference to prev. transform: 10.8168
Iteration: 3
- warping source and target (sqrt)
- compute new registration
- constructAb: -- allocating 1Mb mem for indexing ... done! -- compute derivatives ... done! -- size 60 60 60 ( 6986 non-zero voxels )
- compute robust estimate ( sat 4.685 )... Step: 3 ERR: 13.146 weights average: 0.638882 zero: 0.319353 DONE
- store transform -- old difference to prev. transform: 4.06139 -- difference to prev. transform: 5.55399
Iteration: 4
- warping source and target (sqrt)
- compute new registration
- constructAb: -- allocating 1Mb mem for indexing ... done! -- compute derivatives ... done! -- size 60 60 60 ( 5786 non-zero voxels )
- compute robust estimate ( sat 4.685 )... Step: 15 ERR:
8.50182 weights average: 0.63872 zero: 0.325268 DONE
- store transform -- old difference to prev. transform: 4.50305 -- difference to prev. transform: 4.73783
Iteration: 5
- warping source and target (sqrt)
- compute new registration
- constructAb: -- allocating 1Mb mem for indexing ... done! -- compute derivatives ... done! -- size 60 60 60 ( 4727 non-zero voxels )
- compute robust estimate ( sat 4.685 )... Step: 4 ERR: 6.22319 weights average: 0.641096 zero: 0.327269 DONE
- store transform -- old difference to prev. transform: 6.68849 -- difference to prev. transform: 6.92671 -- 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 ( 24663 non-zero voxels )
- compute robust estimate ( sat 4.685 )... Step: 4 ERR: 485.301 weights average: 0.787986 zero: 0.0833637 DONE
- store transform -- old difference to prev. transform: 19.0035 -- difference to prev. transform: 11.5261
Iteration: 2
- warping source and target (sqrt)
- compute new registration
- constructAb: -- allocating 8Mb mem for indexing ... done! -- compute derivatives ... done! -- size 124 124 124 ( 17729 non-zero voxels )
- compute robust estimate ( sat 4.685 )... Step: 3 ERR: 241.516 weights average: 0.745962 zero: 0.155113 DONE
- store transform -- old difference to prev. transform: 22.2147 -- difference to prev. transform: 12.4584
Iteration: 3
- warping source and target (sqrt)
- compute new registration
- constructAb: -- allocating 8Mb mem for indexing ... done! -- compute derivatives ... done! -- size 124 124 124 ( 11871 non-zero voxels )
- compute robust estimate ( sat 4.685 )... Step: 3 ERR: 53.4814 weights average: 0.693139 zero: 0.244882 DONE
- store transform -- old difference to prev. transform: 16.0371 -- difference to prev. transform: 9.08422
Iteration: 4
- warping source and target (sqrt)
- compute new registration
- constructAb: -- allocating 8Mb mem for indexing ... done! -- compute derivatives ... done! -- size 124 124 124 ( 8228 non-zero voxels )
- compute robust estimate ( sat 4.685 )... Step: 3 ERR: 13.6448 weights average: 0.660016 zero: 0.293024 DONE
- store transform -- old difference to prev. transform: 10.5501 -- difference to prev. transform: 6.29427
Iteration: 5
- warping source and target (sqrt)
- compute new registration
- constructAb: -- allocating 8Mb mem for indexing ... done! -- compute derivatives ... done! -- size 124 124 124 ( 6097 non-zero voxels )
- compute robust estimate ( sat 4.685 )... Step: 5 ERR: 3.4466 weights average: 0.645146 zero: 0.318681 DONE
- store transform -- old difference to prev. transform: 4.42548 -- difference to prev. transform: 3.9269 -- adjusting half-way maps
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 ( 35756 non-zero voxels )
- compute robust estimate ( sat 4.685 )... Step: 3 ERR: 49.1283 weights average: 0.681103 zero: 0.261439 DONE
- store transform -- old difference to prev. transform: 14.8937 -- difference to prev. transform: 7.19314
Iteration: 2
- warping source and target (sqrt)
- compute new registration
- constructAb: -- allocating 64Mb mem for indexing ... done! -- compute derivatives ... done! -- size 252 252 252 ( 25635 non-zero voxels )
- compute robust estimate ( sat 4.685 )... Step: 3 ERR: 14.8053 weights average: 0.671285 zero: 0.283909 DONE
- store transform -- old difference to prev. transform: 9.43798 -- difference to prev. transform: 5.37094
Iteration: 3
- warping source and target (sqrt)
- compute new registration
- constructAb: -- allocating 64Mb mem for indexing ... done! -- compute derivatives ... done! -- size 252 252 252 ( 19866 non-zero voxels )
- compute robust estimate ( sat 4.685 )... Step: 3 ERR: 4.43877 weights average: 0.658105 zero: 0.301923 DONE
- store transform -- old difference to prev. transform: 6.05639 -- difference to prev. transform: 4.00531
Iteration: 4
- warping source and target (sqrt)
- compute new registration
- constructAb: -- allocating 64Mb mem for indexing ... done! -- compute derivatives ... done! -- size 252 252 252 ( 16099 non-zero voxels )
- compute robust estimate ( sat 4.685 )... Step: 3 ERR: 1.55288 weights average: 0.652638 zero: 0.311572 DONE
- store transform -- old difference to prev. transform: 5.05701 -- difference to prev. transform: 3.90321
Iteration: 5
- warping source and target (sqrt)
- compute new registration
- constructAb: -- allocating 64Mb mem for indexing ... done! -- compute derivatives ... done! -- size 252 252 252 ( 0 non-zero voxels )
- compute robust estimate ( sat 4.685 )...MatrixCopyRegion: bad
source region (1,1) --> (6,0)
Linux dnode49.mayo.edu 2.6.18-92.1.6.el5 #1 SMP Wed Jun 25 13:45:47 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Mon Jun 21 11:31:36 CDT 2010
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