Freesurfer June 2010

freesurfer@nmr.mgh.harvard.edu

97 participants
138 discussions

MatrixCopyRegion: bad source region error
by Guang Zeng 21 Jun '10

21 Jun '10

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 buffers cached 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 _________________________________________________________________ The New Busy is not the old busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:…

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Control point editing
by York, Philip 21 Jun '10

21 Jun '10

Hello, I have just edited 12 control points in the OFC/Gyrus rectus area of one of our subjects. I added 12 control points, all to regions of WM that were below 110 and I was very pleased with the output for that region once I ran -autorecon2-cp -autorecon3. However, this resulted in the temporal lobe on the same side to be almost completely neglected by the wm/pial surfaces. Areas that were originally considered WM (even though many areas were below 110 intensity) are now completely left out. What could be the cause of this? Am I changing the intensity threshold globally by editing the control points in one region? Thank you in advance, Philip

2 1

mni or tal to brodmann's
by Corey Keller 21 Jun '10

21 Jun '10

Hi freesurfers, I am wondering if there is a function in freesurfer to convert mni or talairach coordinates to brodmann's areas. I am hoping to input my RAS coordinates, transform them to either mni or talairach (which I know how to do), and then convert to and output the brodmann area. Thanks in advance. Best, Corey

2 1

Longitudinal processing; problem with template creation
by Per Selnes 21 Jun '10

21 Jun '10

Hi, I keep having problems when processing templates in the longitudinal run in FreeSurfer 4.5 on 64bit Linux. For most subjects, the templates seem nearly perfect, but for some, even though the time point recons seem fine, the surfaces of the templates are completely garbled, and it seems as if the posterior part of the brain is chopped off, i.e. outside the image. See enclosed screenshot with the two time points above, and the template below. According to the log, recon-all completed without errors. Might this be related to this post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12187.html Thanks a lot in advance! Regards, Per Selnes

2 1

Re: [Freesurfer] extracting anatomical ROI in native space
by Doug Greve 19 Jun '10

19 Jun '10

Try using nifti output, ie, "--o label1.nii" doug On Sat, 19 Jun 2010, Hwee Ling Lee wrote: > Dear all, > > > > Apologies for my ignorance. > > I'm trying to extract the transverse gyrus, transverse sulcus, planum > temporale and temporal pole from the inflated surface created by freesurfer. > What I intend to do, is to convert these labels into spm analyze format > files in native space, and apply the deformation parameters from DARTEL into > standard space. > > > > Until now, I have created new labels for these regions, and using the > mri_label2vol command line: > > > > mri_label2vol -label subject/label/label1.label -temp subject/orig.mgz > -fillthresh .5 -o label1.bshort > > > > However, it prompted me for a register.dat file and I do not have this. > Using the advice from Dr. Doug Greve, I have tried to use the -identity: > > > > mri_label2vol -label subject/label/label1.label -temp subject/orig.mgz > -identity -fillthresh .5 -o label1.bshort > > > > When I did this, I get 256 files for label1. > > > > So I think I might have done something wrong here. > > > > Could someone please advise me how to do this? I'm lost here. > > Thank you very much in advance! > > > > Best regards, > > HweeLing > > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

1 0

extracting anatomical ROI in native space
by Hwee Ling Lee 19 Jun '10

19 Jun '10

Dear all, Apologies for my ignorance. I'm trying to extract the transverse gyrus, transverse sulcus, planum temporale and temporal pole from the inflated surface created by freesurfer. What I intend to do, is to convert these labels into spm analyze format files in native space, and apply the deformation parameters from DARTEL into standard space. Until now, I have created new labels for these regions, and using the mri_label2vol command line: mri_label2vol -label subject/label/label1.label -temp subject/orig.mgz -fillthresh .5 -o label1.bshort However, it prompted me for a register.dat file and I do not have this. Using the advice from Dr. Doug Greve, I have tried to use the -identity: mri_label2vol -label subject/label/label1.label -temp subject/orig.mgz -identity -fillthresh .5 -o label1.bshort When I did this, I get 256 files for label1. So I think I might have done something wrong here. Could someone please advise me how to do this? I'm lost here. Thank you very much in advance! Best regards, HweeLing

1 0

2nd Level Analyses in FreeSurfer
by Andrew Jahn 18 Jun '10

18 Jun '10

Hi all, I am interested in using Freesurfer to project volume data onto the inflated brains run through the FS pipeline. I am using SPM and have been able to project 1st level con and spmT images onto the corresponding subject's inflated anatomical. My question is, if I wanted to look at 2nd level SPM results on an inflated brain, would it make the most sense to project them onto fsaverage? For example, spmregister --s fsaverage --mov spmT_0001.hdr --reg register.dat Or, is there a way to average the surfaces of the subjects in the study and then project their second levels onto that averaged surface? Thanks! -Andrew

2 1

MAP FUNCTIONAL OF SINGLE SUBJECTS INTO TAILARACH (MNI305) SPACE (fsaverage)
by caspari＠clipper.ens.fr 18 Jun '10

18 Jun '10

Hi! This is maybe something very easy: but I am not sure whether I did it the right way: To map the activation from the subject anatomy to the fsaverage volume I used the sig.nii file out of my contrast folder (humBod-vs_humObj) together with the command mri_vol2vol: mri_vol2vol --mov ../all_days_ss2/bold/all_days_ss2/humBod_vs_humObj/sig.nii --reg ../all_days_ss2/bold/register.dat --o HB-HO-in-tal.2mm_ss2.nii --tal --talres 2 (my functional image is also 2mm isotropic) Can this be done like that? When I remapp the volume activation of my single subject (which has been remapped by the above command onto fsaverage space?) onto the fsaverage surface, and visualize it with tksurfer, actually my main activation (ROI of interest) nearly dissappears, but all the rest looks quite similar- how can this be? I'm not sure whether I proceed in the right way. would be great If someone could help me out! Natalie xxx

2 1

are paired compairisons possible using QDEC
by Mira Michelle Raman 18 Jun '10

18 Jun '10

Hi, I have a group of siblings (one disorder, one unaffected). Is it possible for me to set up the group analysis in a way so that siblings are compared to their sibling, something analogous to a paired t-test, and if so do you have a tutorial or example to which you could direct me. Thank you, Mira Mira Michelle Raman Scientific Programmer Center for Interdisciplinary Brain Sciences Research Stanford University 401 Quarry Rd. Stanford, CA 94305 (650)498-4620

2 1

Parametrics in FreeSurfer
by Andrew Jahn 18 Jun '10

18 Jun '10

Hi FreeSurfer experts, I was wondering whether you are able to use parametric modulators during FS-FAST. All I can see from the mkanalysis-sess gui is setting up contrasts, but I would also like to see how other parameters affect the size and shape of the bold response. Is there any way to do this in Freesurfer? If not, is there a way to visualize parametric analyses done in another software package (e.g., SPM) on a brain processed in freesurfer? Thanks! -Andrew

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Freesurfer June 2010