Fri Jul 9 15:55:57 EDT 2010 /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner /PROJECTS/TOBIASS/SPM_software/freesurfer/bin/recon-all -s bittner -i /home/tobiass/Desktop/FreeSurfer_SLE/NPSLE/D1/pa8/st0/se0/im0 -i /home/tobiass/Desktop/FreeSurfer_SLE/NPSLE/D1/pa8/st1/se0/im0 subjid bittner setenv SUBJECTS_DIR /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE FREESURFER_HOME /PROJECTS/TOBIASS/SPM_software/freesurfer Actual FREESURFER_HOME /PROJECTS/TOBIASS/SPM_software/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 Linux rhea.med.umich.edu 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 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 57344 total used free shared buffers cached Mem: 6038912 2902768 3136144 0 52008 2176976 -/+ buffers/cache: 673784 5365128 Swap: 8159224 0 8159224 ######################################## 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: 2010/07/09-19:55:57-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.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: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.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: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 unknown option -ALL-INFO ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.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: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.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: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/07/09-19:55:58-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.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 ####################################### /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner mri_convert /home/tobiass/Desktop/FreeSurfer_SLE/NPSLE/D1/pa8/st0/se0/im0 /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/001.mgz mri_convert /home/tobiass/Desktop/FreeSurfer_SLE/NPSLE/D1/pa8/st0/se0/im0 /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/001.mgz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /home/tobiass/Desktop/FreeSurfer_SLE/NPSLE/D1/pa8/st0/se0/im0... Starting DICOMRead2() dcmfile = /home/tobiass/Desktop/FreeSurfer_SLE/NPSLE/D1/pa8/st0/se0/im0 dcmdir = /home/tobiass/Desktop/FreeSurfer_SLE/NPSLE/D1/pa8/st0/se0 Ref Series No = 301 Found 171 files, checking for dicoms Found 169 dicom files in series. First Sorting Computing Slice Direction Vs: -0.99942 -0.0270233 0.0201399 Vs: -0.999432 -0.0270236 0.0201402 Second Sorting Counting frames nframes = 1 nslices = 169 ndcmfiles = 169 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=9.80, TE=4.59, TI=0.00, flip angle=8.00 i_ras = (0.0268457, -0.999599, 0.00896871) j_ras = (0.0203743, -0.00842295, -0.999757) k_ras = (0.999432, 0.0270236, 0.0201402) writing to /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/001.mgz... /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner mri_convert /home/tobiass/Desktop/FreeSurfer_SLE/NPSLE/D1/pa8/st1/se0/im0 /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/002.mgz mri_convert /home/tobiass/Desktop/FreeSurfer_SLE/NPSLE/D1/pa8/st1/se0/im0 /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/002.mgz $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /home/tobiass/Desktop/FreeSurfer_SLE/NPSLE/D1/pa8/st1/se0/im0... Starting DICOMRead2() dcmfile = /home/tobiass/Desktop/FreeSurfer_SLE/NPSLE/D1/pa8/st1/se0/im0 dcmdir = /home/tobiass/Desktop/FreeSurfer_SLE/NPSLE/D1/pa8/st1/se0 Ref Series No = 301 Found 172 files, checking for dicoms Found 170 dicom files in series. First Sorting Computing Slice Direction Vs: -0.998672 -0.0513086 -0.00460434 Vs: -0.998672 -0.0513086 -0.00460434 Second Sorting Counting frames nframes = 1 nslices = 170 ndcmfiles = 170 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data TR=9.79, TE=4.59, TI=0.00, flip angle=8.00 i_ras = (0.0514148, -0.998311, 0.0270323) j_ras = (-0.00321185, -0.0272333, -0.999624) k_ras = (0.998672, 0.0513086, -0.00460434) writing to /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/002.mgz... #------------------------------------------ recon-all finished without error at Fri Jul 9 15:56:06 EDT 2010 New invocation of recon-all Fri Jul 9 16:41:49 EDT 2010 /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner /PROJECTS/TOBIASS/SPM_software/freesurfer/bin/recon-all -s bittner -all subjid bittner setenv SUBJECTS_DIR /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE FREESURFER_HOME /PROJECTS/TOBIASS/SPM_software/freesurfer Actual FREESURFER_HOME /PROJECTS/TOBIASS/SPM_software/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 Linux rhea.med.umich.edu 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 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 57344 total used free shared buffers cached Mem: 6038912 4601452 1437460 0 55104 3119072 -/+ buffers/cache: 1427276 4611636 Swap: 8159224 0 8159224 ######################################## 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: 2010/07/09-20:41:50-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.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: 2010/07/09-20:41:51-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.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: 2010/07/09-20:41:52-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-20:41:52-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-20:41:52-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-20:41:52-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-20:41:52-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-20:41:52-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-20:41:52-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-20:41:52-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-20:41:52-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 unknown option -ALL-INFO ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-20:41:52-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-20:41:52-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-20:41:52-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-20:41:53-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-20:41:53-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-20:41:53-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-20:41:53-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-20:41:53-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-20:41:53-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-20:41:53-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-20:41:53-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-20:41:53-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-20:41:53-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-20:41:54-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-20:41:54-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-20:41:54-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-20:41:54-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.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: 2010/07/09-20:41:54-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.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: 2010/07/09-20:41:54-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/09-20:41:54-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/07/09-20:41:54-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/07/09-20:41:54-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: tobiass Machine: rhea.med.umich.edu Platform: Linux PlatformVersion: 2.6.18-128.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 ####################################### #-------------------------------------------- #@# MotionCor Fri Jul 9 16:41:56 EDT 2010 Found 2 runs /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/001.mgz /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/002.mgz /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner mri_motion_correct.fsl -o /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/rawavg.mgz -wild /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/001.mgz /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/002.mgz tmpdir is /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480 -------------------------------------------------------------- mri_motion_correct.fsl logfile is /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/rawavg.mgz.mri_motion_correct.fsl.log -------------------------------------------------------------- WARNING: TRs are inconsistent 9.804 9.7898 WARNING: TEs are inconsistent 4.594 4.5921 ----------------------------------------- Converting /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/001.mgz Fri Jul 9 16:42:19 EDT 2010 /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner mri_convert /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/001.mgz /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/cor-1.img -odt float $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/001.mgz... TR=9.80, TE=4.59, TI=0.00, flip angle=8.00 i_ras = (0.0268457, -0.999599, 0.00896871) j_ras = (0.0203743, -0.00842295, -0.999757) k_ras = (0.999432, 0.0270236, 0.0201402) changing data type from 4 to 3 (noscale = 0)... writing to /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/cor-1.img... Analyze Output Matrix 0.024 0.018 0.999 -99.739; -0.877 -0.007 0.027 144.804; 0.008 -0.877 0.020 123.914; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/002.mgz Fri Jul 9 16:42:25 EDT 2010 /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner mri_convert /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/002.mgz /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/cor-2.img -odt float $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/002.mgz... TR=9.79, TE=4.59, TI=0.00, flip angle=8.00 i_ras = (0.0514148, -0.998311, 0.0270323) j_ras = (-0.00321185, -0.0272333, -0.999624) k_ras = (0.998672, 0.0513086, -0.00460434) changing data type from 4 to 3 (noscale = 0)... writing to /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/cor-2.img... Analyze Output Matrix 0.046 -0.003 0.999 -99.067; -0.884 -0.024 0.051 136.288; 0.024 -0.885 -0.005 150.557; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Motion Correcting /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/cor-2.img Fri Jul 9 16:42:28 EDT 2010 /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner fsl_rigid_register -maxangle 90 -r /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/cor-1.img -i /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/cor-2.img -o /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/resampled.img -tmpdir /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480 -cleanup $Id: fsl_rigid_register,v 1.26.2.1 2008/08/12 23:38:57 nicks Exp $ Fri Jul 9 16:42:30 EDT 2010 /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/resampled.img -------------------------------------- /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner mri_convert /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/cor-1.img /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/refvol.fsl_rigid_register.nii mri_convert /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/cor-1.img /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/refvol.fsl_rigid_register.nii $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/cor-1.img... TR=9.80, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0268457, -0.999599, 0.00896871) j_ras = (0.0203743, -0.00842295, -0.999757) k_ras = (0.999432, 0.0270236, 0.0201402) writing to /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/refvol.fsl_rigid_register.nii... -------------------------------------- /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner mri_convert /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/cor-2.img /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/invol.fsl_rigid_register.nii mri_convert /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/cor-2.img /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/invol.fsl_rigid_register.nii $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/cor-2.img... TR=9.79, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0514148, -0.998311, 0.0270323) j_ras = (-0.00321185, -0.0272333, -0.999624) k_ras = (0.998672, 0.0513086, -0.00460434) writing to /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/invol.fsl_rigid_register.nii... -------------------------------------- /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner tkregister2_cmdl --targ /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/cor-1.img --mov /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/cor-2.img --reg /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/tkregister.dat --fslregout /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/initxfm.fslmat --regheader --noedit --s doesnotmatter tkregister_tcl /PROJECTS/TOBIASS/SPM_software/freesurfer/lib/tcl/tkregister2.tcl target volume /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/cor-1.img movable volume /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/cor-2.img reg file /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/tkregister.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.86.2.12 2009/03/19 22:04:20 greve Exp $ Diagnostic Level -1 INFO: loading target /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/cor-1.img INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/cor-2.img Tmov: -------------------- -0.885 0.000 0.000 127.490; 0.000 0.000 1.000 -85.000; 0.000 -0.885 0.000 127.490; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- -0.051 0.998 -0.027 10.591; 0.999 0.051 -0.005 -0.663; 0.003 0.027 1.000 -25.425; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- -0.051 0.998 -0.027 10.591; 0.999 0.051 -0.005 -0.663; 0.003 0.027 1.000 -25.425; 0.000 0.000 0.000 1.000; Determinant -1 subject = doesnotmatter RegMat --------------------------- 1.000 -0.025 -0.018 10.591; 0.025 0.999 -0.025 -0.663; 0.018 0.024 1.000 -25.425; 0.000 0.000 0.000 1.000; register: file /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/tkregister.dat written FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = 0.783838, ref det = 0.76957 INFO: FSL2FreeSurfer: Mov volume is NIFTI with positive det, applying LR flip to registration matrix. INFO: FSL2FreeSurfer: Ref volume is NIFTI with positive det, applying LR flip to registration matrix. Init FSL Mat based on geometry ------------------- 0.99953419 -0.01817076 0.02451760 -10.97357941 0.01756949 0.99954480 0.02451837 -30.99892426 -0.02495357 -0.02407832 0.99939883 7.31883860 0.00000000 0.00000000 0.00000000 1.00000000 ------------------------------------------------- -------------------------------------- /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner calling eval flirt -in /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/invol.fsl_rigid_register.hdr -out /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/outvol.fsl_rigid_register.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/refvol.fsl_rigid_register.hdr -init /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/initxfm.fslmat -omat /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/outvol.fsl_rigid_register.fslmat -------------------------------------- /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner mri_convert /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/outvol.fsl_rigid_register.nii /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/resampled.img mri_convert /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/outvol.fsl_rigid_register.nii /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/resampled.img $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/outvol.fsl_rigid_register.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0268457, -0.999599, 0.00896871) j_ras = (0.0203743, -0.00842295, -0.999757) k_ras = (0.999432, 0.0270236, 0.0201402) writing to /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/resampled.img... Analyze Output Matrix 0.024 0.018 0.999 -99.739; -0.877 -0.007 0.027 144.804; 0.008 -0.877 0.020 123.914; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 Started at Fri Jul 9 16:42:30 EDT 2010 Ended at Fri Jul 9 16:49:14 EDT 2010 fsl_rigid_register Done To check results, run: tkmedit -f /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/cor-1.img -aux /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/resampled.img mv /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/resampled.img /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/cor-2.img ----------------------------------------- Averaging Fri Jul 9 16:49:14 EDT 2010 /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner inhibiting isotropic volume interpolation 1 of 2: reading /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/cor-1.img... 2 of 2: reading /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/cor-2.img... ERROR: premature end of file ERROR: Success (0) frame = 0, slice = 169, k=169, row = 0 nread = 0, nexpected = 288 fname = height = 288 width = 288 depth = 170 nframe = 1 imnr0 = 1 imnr1 = 170 xnum = 288 ynum = 288 fov = 288.000000 thick = 1.000000 xstart = -144.000000 xend = 144.000000 ystart = -144.000000 yend = 144.000000 zstart = -85.000000 zend = 85.000000 type = 3 xsize = 0.885346 ysize = 0.885346 zsize = 1.000000 x ras = 0.051415 -0.998311 0.027032 y ras = -0.003212 -0.027233 -0.999624 z ras = 0.998672 0.051309 -0.004604 c ras = -6.993301 9.046333 25.304390 det(xyz_ras) = 1.000000 ras_good_flag = 1 brightness = 1 subject_name = path_to_t1 = fname_format = analyzeRead2(): error reading from file /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/cor-2.img mri_average: MRIread(/PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-28480/cor-2.img) failed Linux rhea.med.umich.edu 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Jul 9 16:49:27 EDT 2010 New invocation of recon-all Fri Jul 16 15:09:32 EDT 2010 /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner /PROJECTS/TOBIASS/SPM_software/freesurfer/bin/recon-all -s /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner -motioncor subjid bittner setenv SUBJECTS_DIR /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE FREESURFER_HOME /PROJECTS/TOBIASS/SPM_software/freesurfer Actual FREESURFER_HOME /PROJECTS/TOBIASS/SPM_software/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 Linux titan 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 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 57344 total used free shared buffers cached Mem: 6038912 5198136 840776 0 6248 2465836 -/+ buffers/cache: 2726052 3312860 Swap: 8159224 192 8159032 ######################################## 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: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.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: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.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: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 unknown option -ALL-INFO ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.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: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.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: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/07/16-19:09:33-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.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 ####################################### #-------------------------------------------- #@# MotionCor Fri Jul 16 15:09:33 EDT 2010 Found 2 runs /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/001.mgz /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/002.mgz /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner mri_motion_correct.fsl -o /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/rawavg.mgz -wild /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/001.mgz /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/002.mgz tmpdir is /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422 -------------------------------------------------------------- mri_motion_correct.fsl logfile is /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/rawavg.mgz.mri_motion_correct.fsl.log -------------------------------------------------------------- WARNING: TRs are inconsistent 9.804 9.7898 WARNING: TEs are inconsistent 4.594 4.5921 ----------------------------------------- Converting /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/001.mgz Fri Jul 16 15:09:41 EDT 2010 /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner mri_convert /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/001.mgz /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/cor-1.img -odt float $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/001.mgz... TR=9.80, TE=4.59, TI=0.00, flip angle=8.00 i_ras = (0.0268457, -0.999599, 0.00896871) j_ras = (0.0203743, -0.00842295, -0.999757) k_ras = (0.999432, 0.0270236, 0.0201402) changing data type from 4 to 3 (noscale = 0)... writing to /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/cor-1.img... Analyze Output Matrix 0.024 0.018 0.999 -99.739; -0.877 -0.007 0.027 144.804; 0.008 -0.877 0.020 123.914; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/002.mgz Fri Jul 16 15:09:44 EDT 2010 /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner mri_convert /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/002.mgz /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/cor-2.img -odt float $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/002.mgz... TR=9.79, TE=4.59, TI=0.00, flip angle=8.00 i_ras = (0.0514148, -0.998311, 0.0270323) j_ras = (-0.00321185, -0.0272333, -0.999624) k_ras = (0.998672, 0.0513086, -0.00460434) changing data type from 4 to 3 (noscale = 0)... writing to /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/cor-2.img... Analyze Output Matrix 0.046 -0.003 0.999 -99.067; -0.884 -0.024 0.051 136.288; 0.024 -0.885 -0.005 150.557; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Motion Correcting /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/cor-2.img Fri Jul 16 15:09:47 EDT 2010 /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner fsl_rigid_register -maxangle 90 -r /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/cor-1.img -i /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/cor-2.img -o /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/resampled.img -tmpdir /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422 -cleanup $Id: fsl_rigid_register,v 1.26.2.1 2008/08/12 23:38:57 nicks Exp $ Fri Jul 16 15:09:47 EDT 2010 /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/resampled.img -------------------------------------- /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner mri_convert /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/cor-1.img /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/refvol.fsl_rigid_register.nii mri_convert /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/cor-1.img /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/refvol.fsl_rigid_register.nii $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/cor-1.img... TR=9.80, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0268457, -0.999599, 0.00896871) j_ras = (0.0203743, -0.00842295, -0.999757) k_ras = (0.999432, 0.0270236, 0.0201402) writing to /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/refvol.fsl_rigid_register.nii... -------------------------------------- /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner mri_convert /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/cor-2.img /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/invol.fsl_rigid_register.nii mri_convert /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/cor-2.img /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/invol.fsl_rigid_register.nii $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/cor-2.img... TR=9.79, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0514148, -0.998311, 0.0270323) j_ras = (-0.00321185, -0.0272333, -0.999624) k_ras = (0.998672, 0.0513086, -0.00460434) writing to /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/invol.fsl_rigid_register.nii... -------------------------------------- /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner tkregister2_cmdl --targ /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/cor-1.img --mov /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/cor-2.img --reg /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/tkregister.dat --fslregout /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/initxfm.fslmat --regheader --noedit --s doesnotmatter tkregister_tcl /PROJECTS/TOBIASS/SPM_software/freesurfer/lib/tcl/tkregister2.tcl target volume /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/cor-1.img movable volume /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/cor-2.img reg file /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/tkregister.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.86.2.12 2009/03/19 22:04:20 greve Exp $ Diagnostic Level -1 INFO: loading target /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/cor-1.img INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/cor-2.img Tmov: -------------------- -0.885 0.000 0.000 127.490; 0.000 0.000 1.000 -85.000; 0.000 -0.885 0.000 127.490; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- -0.051 0.998 -0.027 10.591; 0.999 0.051 -0.005 -0.663; 0.003 0.027 1.000 -25.425; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- -0.051 0.998 -0.027 10.591; 0.999 0.051 -0.005 -0.663; 0.003 0.027 1.000 -25.425; 0.000 0.000 0.000 1.000; Determinant -1 subject = doesnotmatter RegMat --------------------------- 1.000 -0.025 -0.018 10.591; 0.025 0.999 -0.025 -0.663; 0.018 0.024 1.000 -25.425; 0.000 0.000 0.000 1.000; register: file /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/tkregister.dat written FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = 0.783838, ref det = 0.76957 INFO: FSL2FreeSurfer: Mov volume is NIFTI with positive det, applying LR flip to registration matrix. INFO: FSL2FreeSurfer: Ref volume is NIFTI with positive det, applying LR flip to registration matrix. Init FSL Mat based on geometry ------------------- 0.99953419 -0.01817076 0.02451760 -10.97357941 0.01756949 0.99954480 0.02451837 -30.99892426 -0.02495357 -0.02407832 0.99939883 7.31883860 0.00000000 0.00000000 0.00000000 1.00000000 ------------------------------------------------- -------------------------------------- /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner calling eval flirt -in /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/invol.fsl_rigid_register.hdr -out /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/outvol.fsl_rigid_register.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/refvol.fsl_rigid_register.hdr -init /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/initxfm.fslmat -omat /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/outvol.fsl_rigid_register.fslmat -------------------------------------- /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner mri_convert /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/outvol.fsl_rigid_register.nii /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/resampled.img mri_convert /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/outvol.fsl_rigid_register.nii /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/resampled.img $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/outvol.fsl_rigid_register.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0268457, -0.999599, 0.00896871) j_ras = (0.0203743, -0.00842295, -0.999757) k_ras = (0.999432, 0.0270236, 0.0201402) writing to /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/resampled.img... Analyze Output Matrix 0.024 0.018 0.999 -99.739; -0.877 -0.007 0.027 144.804; 0.008 -0.877 0.020 123.914; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 Started at Fri Jul 16 15:09:47 EDT 2010 Ended at Fri Jul 16 15:11:52 EDT 2010 fsl_rigid_register Done To check results, run: tkmedit -f /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/cor-1.img -aux /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/resampled.img mv /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/resampled.img /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/cor-2.img ----------------------------------------- Averaging Fri Jul 16 15:11:52 EDT 2010 /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner inhibiting isotropic volume interpolation 1 of 2: reading /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/cor-1.img... 2 of 2: reading /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/cor-2.img... ERROR: premature end of file ERROR: Success (0) frame = 0, slice = 169, k=169, row = 0 nread = 0, nexpected = 288 fname = height = 288 width = 288 depth = 170 nframe = 1 imnr0 = 1 imnr1 = 170 xnum = 288 ynum = 288 fov = 288.000000 thick = 1.000000 xstart = -144.000000 xend = 144.000000 ystart = -144.000000 yend = 144.000000 zstart = -85.000000 zend = 85.000000 type = 3 xsize = 0.885346 ysize = 0.885346 zsize = 1.000000 x ras = 0.051415 -0.998311 0.027032 y ras = -0.003212 -0.027233 -0.999624 z ras = 0.998672 0.051309 -0.004604 c ras = -6.993301 9.046333 25.304390 det(xyz_ras) = 1.000000 ras_good_flag = 1 brightness = 1 subject_name = path_to_t1 = fname_format = analyzeRead2(): error reading from file /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/cor-2.img mri_average: MRIread(/PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-5422/cor-2.img) failed Linux titan 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Jul 16 15:11:57 EDT 2010 New invocation of recon-all Mon Jul 19 09:50:20 EDT 2010 /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner /PROJECTS/TOBIASS/SPM_software/freesurfer/bin/recon-all -s /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner -motioncor subjid bittner setenv SUBJECTS_DIR /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE FREESURFER_HOME /PROJECTS/TOBIASS/SPM_software/freesurfer Actual FREESURFER_HOME /PROJECTS/TOBIASS/SPM_software/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 Linux titan 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 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 57344 total used free shared buffers cached Mem: 6038912 5993984 44928 0 3404 4906620 -/+ buffers/cache: 1083960 4954952 Swap: 8159224 192 8159032 ######################################## 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: 2010/07/19-13:50:20-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.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: 2010/07/19-13:50:21-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.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: 2010/07/19-13:50:21-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/19-13:50:22-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/19-13:50:22-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/19-13:50:22-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/19-13:50:23-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/19-13:50:23-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/19-13:50:23-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/19-13:50:23-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/19-13:50:23-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 unknown option -ALL-INFO ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/19-13:50:24-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/19-13:50:24-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/19-13:50:24-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/19-13:50:24-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/19-13:50:25-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/19-13:50:25-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/19-13:50:25-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/19-13:50:25-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/19-13:50:26-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/19-13:50:26-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/19-13:50:26-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/19-13:50:27-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/19-13:50:27-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/19-13:50:27-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/19-13:50:27-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/19-13:50:28-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/19-13:50:28-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.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: 2010/07/19-13:50:28-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.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: 2010/07/19-13:50:29-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable4 $ TimeStamp: 2010/07/19-13:50:29-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/07/19-13:50:29-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2010/07/19-13:50:29-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: tobiass Machine: titan Platform: Linux PlatformVersion: 2.6.18-128.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 ####################################### #-------------------------------------------- #@# MotionCor Mon Jul 19 09:50:30 EDT 2010 Found 2 runs /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/001.mgz /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/002.mgz /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner mri_motion_correct.fsl -o /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/rawavg.mgz -wild /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/001.mgz /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/002.mgz tmpdir is /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287 -------------------------------------------------------------- mri_motion_correct.fsl logfile is /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/rawavg.mgz.mri_motion_correct.fsl.log -------------------------------------------------------------- WARNING: TRs are inconsistent 9.804 9.7898 WARNING: TEs are inconsistent 4.594 4.5921 ----------------------------------------- Converting /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/001.mgz Mon Jul 19 09:50:34 EDT 2010 /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner mri_convert /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/001.mgz /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-1.img -odt float $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/001.mgz... TR=9.80, TE=4.59, TI=0.00, flip angle=8.00 i_ras = (0.0268457, -0.999599, 0.00896871) j_ras = (0.0203743, -0.00842295, -0.999757) k_ras = (0.999432, 0.0270236, 0.0201402) changing data type from 4 to 3 (noscale = 0)... writing to /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-1.img... Analyze Output Matrix 0.024 0.018 0.999 -99.739; -0.877 -0.007 0.027 144.804; 0.008 -0.877 0.020 123.914; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Converting /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/002.mgz Mon Jul 19 09:50:37 EDT 2010 /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner mri_convert /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/002.mgz /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-2.img -odt float $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/orig/002.mgz... TR=9.79, TE=4.59, TI=0.00, flip angle=8.00 i_ras = (0.0514148, -0.998311, 0.0270323) j_ras = (-0.00321185, -0.0272333, -0.999624) k_ras = (0.998672, 0.0513086, -0.00460434) changing data type from 4 to 3 (noscale = 0)... writing to /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-2.img... Analyze Output Matrix 0.046 -0.003 0.999 -99.067; -0.884 -0.024 0.051 136.288; 0.024 -0.885 -0.005 150.557; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 ----------------------------------------- Motion Correcting /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-2.img Mon Jul 19 09:50:39 EDT 2010 /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner fsl_rigid_register -maxangle 90 -r /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-1.img -i /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-2.img -o /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/resampled.img -tmpdir /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287 -cleanup $Id: fsl_rigid_register,v 1.26.2.1 2008/08/12 23:38:57 nicks Exp $ Mon Jul 19 09:50:40 EDT 2010 /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/resampled.img -------------------------------------- /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner mri_convert /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-1.img /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/refvol.fsl_rigid_register.nii mri_convert /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-1.img /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/refvol.fsl_rigid_register.nii $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-1.img... TR=9.80, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0268457, -0.999599, 0.00896871) j_ras = (0.0203743, -0.00842295, -0.999757) k_ras = (0.999432, 0.0270236, 0.0201402) writing to /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/refvol.fsl_rigid_register.nii... -------------------------------------- /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner mri_convert /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-2.img /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/invol.fsl_rigid_register.nii mri_convert /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-2.img /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/invol.fsl_rigid_register.nii $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-2.img... TR=9.79, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0514148, -0.998311, 0.0270323) j_ras = (-0.00321185, -0.0272333, -0.999624) k_ras = (0.998672, 0.0513086, -0.00460434) writing to /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/invol.fsl_rigid_register.nii... -------------------------------------- /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner tkregister2_cmdl --targ /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-1.img --mov /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-2.img --reg /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/tkregister.dat --fslregout /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/initxfm.fslmat --regheader --noedit --s doesnotmatter tkregister_tcl /PROJECTS/TOBIASS/SPM_software/freesurfer/lib/tcl/tkregister2.tcl target volume /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-1.img movable volume /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-2.img reg file /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/tkregister.dat LoadVol 0 ZeroCRAS 0 $Id: tkregister2.c,v 1.86.2.12 2009/03/19 22:04:20 greve Exp $ Diagnostic Level -1 INFO: loading target /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-1.img INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-2.img Tmov: -------------------- -0.885 0.000 0.000 127.490; 0.000 0.000 1.000 -85.000; 0.000 -0.885 0.000 127.490; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) ---- Input registration matrix (computed) -------- -0.051 0.998 -0.027 10.591; 0.999 0.051 -0.005 -0.663; 0.003 0.027 1.000 -25.425; 0.000 0.000 0.000 1.000; --------------------------------------- ---- Input registration matrix -------- -0.051 0.998 -0.027 10.591; 0.999 0.051 -0.005 -0.663; 0.003 0.027 1.000 -25.425; 0.000 0.000 0.000 1.000; Determinant -1 subject = doesnotmatter RegMat --------------------------- 1.000 -0.025 -0.018 10.591; 0.025 0.999 -0.025 -0.663; 0.018 0.024 1.000 -25.425; 0.000 0.000 0.000 1.000; register: file /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/tkregister.dat written FSLOUTPUTTYPE NIFTI tkreg2FSL: mov det = 0.783838, ref det = 0.76957 INFO: FSL2FreeSurfer: Mov volume is NIFTI with positive det, applying LR flip to registration matrix. INFO: FSL2FreeSurfer: Ref volume is NIFTI with positive det, applying LR flip to registration matrix. Init FSL Mat based on geometry ------------------- 0.99953419 -0.01817076 0.02451760 -10.97357941 0.01756949 0.99954480 0.02451837 -30.99892426 -0.02495357 -0.02407832 0.99939883 7.31883860 0.00000000 0.00000000 0.00000000 1.00000000 ------------------------------------------------- -------------------------------------- /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner calling eval flirt -in /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/invol.fsl_rigid_register.hdr -out /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/outvol.fsl_rigid_register.hdr -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -interp trilinear -dof 6 -ref /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/refvol.fsl_rigid_register.hdr -init /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/initxfm.fslmat -omat /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/outvol.fsl_rigid_register.fslmat -------------------------------------- /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner mri_convert /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/outvol.fsl_rigid_register.nii /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/resampled.img mri_convert /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/outvol.fsl_rigid_register.nii /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/resampled.img $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ reading from /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/outvol.fsl_rigid_register.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0268457, -0.999599, 0.00896871) j_ras = (0.0203743, -0.00842295, -0.999757) k_ras = (0.999432, 0.0270236, 0.0201402) writing to /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/resampled.img... Analyze Output Matrix 0.024 0.018 0.999 -99.739; -0.877 -0.007 0.027 144.804; 0.008 -0.877 0.020 123.914; 0.000 0.000 0.000 1.000; -------------------- INFO: set hdr.hist.orient to -1 Started at Mon Jul 19 09:50:40 EDT 2010 Ended at Mon Jul 19 09:52:35 EDT 2010 fsl_rigid_register Done To check results, run: tkmedit -f /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-1.img -aux /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/resampled.img mv /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/resampled.img /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-2.img ----------------------------------------- Averaging Mon Jul 19 09:52:35 EDT 2010 /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner inhibiting isotropic volume interpolation 1 of 2: reading /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-1.img... 2 of 2: reading /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-2.img... ERROR: premature end of file ERROR: Success (0) frame = 0, slice = 169, k=169, row = 0 nread = 0, nexpected = 288 fname = height = 288 width = 288 depth = 170 nframe = 1 imnr0 = 1 imnr1 = 170 xnum = 288 ynum = 288 fov = 288.000000 thick = 1.000000 xstart = -144.000000 xend = 144.000000 ystart = -144.000000 yend = 144.000000 zstart = -85.000000 zend = 85.000000 type = 3 xsize = 0.885346 ysize = 0.885346 zsize = 1.000000 x ras = 0.051415 -0.998311 0.027032 y ras = -0.003212 -0.027233 -0.999624 z ras = 0.998672 0.051309 -0.004604 c ras = -6.993301 9.046333 25.304390 det(xyz_ras) = 1.000000 ras_good_flag = 1 brightness = 1 subject_name = path_to_t1 = fname_format = analyzeRead2(): error reading from file /PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-2.img mri_average: MRIread(/PROJECTS/TOBIASS/SPM_software/freesurfer/subjects/VBM_SLE/NPSLE/bittner/mri/tmp-mri_motion_correct.fsl-25287/cor-2.img) failed Linux titan 2.6.18-128.el5 #1 SMP Wed Dec 17 11:41:38 EST 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Jul 19 09:52:39 EDT 2010