New invocation of recon-all Thu Feb 13 11:55:48 EST 2014 /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13 /usr/local/freesurfer/stable5_3_0/bin/recon-all -autorecon1 -subjid LCS13 subjid LCS13 setenv SUBJECTS_DIR /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI FREESURFER_HOME /usr/local/freesurfer/stable5_3_0 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-v5.3.0-20130514 Linux huygens 2.6.32-431.1.2.0.1.el6.x86_64 #1 SMP Fri Dec 13 13:06:13 UTC 2013 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 4096 memorylocked 64 kbytes maxproc 4096 total used free shared buffers cached Mem: 37006396 24519340 12487056 0 491608 13508832 -/+ buffers/cache: 10518900 26487496 Swap: 8393952 147744 8246208 ######################################## program versions used $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:55:50-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:55:51-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@minerva (x86_64-unknown-linux-gnu) on 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:55:59-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:00-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:00-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:01-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:02-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:03-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:03-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:04-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:05-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:06-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:06-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:07-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:08-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:09-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:09-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:10-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:11-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:11-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:12-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:13-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:13-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:14-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:15-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:16-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:16-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:17-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:18-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:18-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:19-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:22-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:23-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:24-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:25-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:25-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:26-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/02/13-16:56:27-GMT BuildTimeStamp: May 14 2013 15:52:47 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: oboadu Machine: huygens Platform: Linux PlatformVersion: 2.6.32-431.1.2.0.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/stable5_3_0/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /usr/local/freesurfer/stable5_3_0/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### #-------------------------------------------- #@# MotionCor Thu Feb 13 11:56:27 EST 2014 Found 3 runs /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig/001.mgz /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig/002.mgz /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig/003.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13 mri_robust_template --mov /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig/001.mgz /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig/002.mgz /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig/003.mgz --average 1 --template /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig/001-iscale.txt /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig/002-iscale.txt /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig/003-iscale.txt --subsample 200 --lta /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig/001.lta /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig/002.lta /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig/003.lta $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ --mov: Using /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig/001.mgz as movable/source volume. --mov: Using /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig/002.mgz as movable/source volume. --mov: Using /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig/003.mgz as movable/source volume. Total: 3 input volumes --average: Using method 1 for template computation. --template: Using /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig/001.mgz'... converting source '/local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig/002.mgz'... converting source '/local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3 reading source '/local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig/003.mgz'... converting source '/local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig/003.mgz' to bspline ... MRItoBSpline degree 3 MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig/002.mgz ) to TP 1 ( /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig/001.mgz ) -- Original : (1, 1, 1.33) mm size and (256, 256, 195) voxels. -- Resampled: (1, 1, 1) mm size and (256, 256, 260) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (1, 1, 1.33) mm size and (256, 256, 195) voxels. -- Resampled: (1, 1, 1) mm size and (256, 256, 260) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 - Max Resolution used: 2 -- gpS ( 64 , 64 , 65 ) -- gpT ( 64 , 64 , 65 ) - running loop to estimate saturation parameter: Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Adjusting final transform due to non isotropic voxels ... Adjusting final transform due to non isotropic voxels ... [init] ========================= TP 3 to TP 1 ============================== Register TP 3 ( /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig/003.mgz ) to TP 1 ( /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig/001.mgz ) -- Original : (1, 1, 1.33) mm size and (256, 256, 195) voxels. -- Resampled: (1, 1, 1) mm size and (256, 256, 260) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (1, 1, 1.33) mm size and (256, 256, 195) voxels. -- Resampled: (1, 1, 1) mm size and (256, 256, 260) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 - Max Resolution used: 2 -- gpS ( 64 , 64 , 65 ) -- gpT ( 64 , 64 , 65 ) - running loop to estimate saturation parameter: Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Adjusting final transform due to non isotropic voxels ... Adjusting final transform due to non isotropic voxels ... mapping movs and creating initial template... allow intensity scaling using median Writing final template: /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/rawavg.mgz Writing final transforms (warps etc.)... Determinant( lta[ 0 ]) : 1 Determinant( lta[ 1 ]) : 1 Determinant( lta[ 2 ]) : 1 registration took 2 minutes and 11 seconds. Thank you for using RobustTemplate! If you find it useful and use it for a publication, please cite: Within-Subject Template Estimation for Unbiased Longitudinal Image Analysis M. Reuter, N.J. Schmansky, H.D. Rosas, B. Fischl. NeuroImage 2012. http://dx.doi.org/10.1016/j.neuroimage.2012.02.084 http://reuter.mit.edu/papers/reuter-long12.pdf /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13 mri_convert /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/rawavg.mgz /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig.mgz --conform mri_convert /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/rawavg.mgz /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/rawavg.mgz... TR=2730.00, TE=3.39, TI=1000.00, flip angle=7.00 warning: input volume axes are not orthogonal:i_dot_j = 0.000000, i_dot_k = 0.966881, j_dot_k = -0.011045 i_ras = (-1, 6.0529e-17, 9.98875e-17) j_ras = (-6.21908e-17, -0.999862, -0.0165856) k_ras = (-0.966881, 0.00681458, 0.255138) Original Data has (1, 1, 1.33) mm size and (256, 256, 195) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig.mgz... mri_add_xform_to_header -c /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/transforms/talairach.xfm /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig.mgz /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Thu Feb 13 11:58:56 EST 2014 /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Feb 13 12:00:42 EST 2014 /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) INFO: Attempting MINC mritotal to perform Talairach align #-------------------------------------------- #@# Talairach Thu Feb 13 12:00:44 EST 2014 /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri /usr/local/freesurfer/stable5_3_0/bin/talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux huygens 2.6.32-431.1.2.0.1.el6.x86_64 #1 SMP Fri Dec 13 13:06:13 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Thu Feb 13 12:01:33 EST 2014 tmpdir is transforms/tmp.talairach.24986 /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri mri_convert orig_nu.mgz transforms/tmp.talairach.24986/src.mnc mri_convert orig_nu.mgz transforms/tmp.talairach.24986/src.mnc $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig_nu.mgz... TR=2730.00, TE=3.39, TI=1000.00, flip angle=7.00 i_ras = (-1, -3.30872e-24, 0) j_ras = (0, 1.86265e-09, -1) k_ras = (0, 1, 1.86265e-09) writing to transforms/tmp.talairach.24986/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/stable5_3_0/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.24986/src.mnc transforms/talairach.auto.xfm Thu Feb 13 12:01:46 EST 2014 talairach done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Feb 13 12:01:47 EST 2014 /local_mount/space/huygens/1/users/Osei/KristofDavid/MRI/LCS13/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux huygens 2.6.32-431.1.2.0.1.el6.x86_64 #1 SMP Fri Dec 13 13:06:13 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s LCS13 exited with ERRORS at Thu Feb 13 12:01:48 EST 2014 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting