Wed Aug 29 10:55:38 CDT 2012 /projects/d20277/dek/PPMI/done/3157 /projects/d20277/software/freesurfer/bin/recon-all -sd /home/drg/myprojects/dek/PPMI/done -all -noappend -subjid 3157 subjid 3157 setenv SUBJECTS_DIR /projects/d20277/dek/PPMI/done FREESURFER_HOME /projects/d20277/software/freesurfer Actual FREESURFER_HOME /projects/d20277/software/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux qnode0362 2.6.18-128.el5-perfctr #1 SMP Wed Jun 23 11:22:11 CDT 2010 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked unlimited maxproc 409600 total used free shared buffers cached Mem: 49432920 11001836 38431084 0 256 2137364 -/+ buffers/cache: 8864216 40568704 Swap: 0 0 0 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 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: 2012/08/29-15:55:39-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 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: 2012/08/29-15:55:39-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr 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 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:39-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:39-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:39-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:39-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:39-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:39-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:40-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:40-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:40-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:40-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:40-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:40-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:40-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:40-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:40-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:40-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:41-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:42-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-15:55:43-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: drg Machine: qnode0362 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /projects/d20277/software/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /projects/d20277/software/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /projects/d20277/software/freesurfer Previous: /usr/local/freesurfer #-------------------------------------------- #@# MotionCor Wed Aug 29 10:55:44 CDT 2012 Found 1 runs /projects/d20277/dek/PPMI/done/3157/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /projects/d20277/dek/PPMI/done/3157/mri/orig/001.mgz /projects/d20277/dek/PPMI/done/3157/mri/rawavg.mgz /projects/d20277/dek/PPMI/done/3157 mri_convert /projects/d20277/dek/PPMI/done/3157/mri/rawavg.mgz /projects/d20277/dek/PPMI/done/3157/mri/orig.mgz --conform mri_convert /projects/d20277/dek/PPMI/done/3157/mri/rawavg.mgz /projects/d20277/dek/PPMI/done/3157/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from /projects/d20277/dek/PPMI/done/3157/mri/rawavg.mgz... TR=2300.00, TE=2.98, TI=900.00, flip angle=9.00 i_ras = (-0.014028, -0.999902, 1.35409e-08) j_ras = (0.00690176, -9.68411e-05, -0.999976) k_ras = (-0.999878, 0.0140277, -0.00690247) Original Data has (1, 1, 1) mm size and (240, 256, 160) 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 /projects/d20277/dek/PPMI/done/3157/mri/orig.mgz... mri_add_xform_to_header -c /projects/d20277/dek/PPMI/done/3157/mri/transforms/talairach.xfm /projects/d20277/dek/PPMI/done/3157/mri/orig.mgz /projects/d20277/dek/PPMI/done/3157/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Wed Aug 29 10:56:00 CDT 2012 /projects/d20277/dek/PPMI/done/3157/mri talairach_avi --i orig.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 Wed Aug 29 10:56:45 CDT 2012 /projects/d20277/dek/PPMI/done/3157/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.4067, pval=0.0643 >= threshold=0.0050) awk -f /projects/d20277/software/freesurfer/bin/extract_talairach_avi_QA.awk /projects/d20277/dek/PPMI/done/3157/mri/transforms/talairach_avi.log TalAviQA: 0.97362 z-score: -1 #-------------------------------------------- #@# Nu Intensity Correction Wed Aug 29 10:56:46 CDT 2012 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /projects/d20277/dek/PPMI/done/3157/mri /projects/d20277/software/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18 2011/03/02 20:16:39 nicks Exp $ Linux qnode0362 2.6.18-128.el5-perfctr #1 SMP Wed Jun 23 11:22:11 CDT 2010 x86_64 x86_64 x86_64 GNU/Linux Wed Aug 29 10:56:46 CDT 2012 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 tmpdir is ./tmp.mri_nu_correct.mni.603 /projects/d20277/dek/PPMI/done/3157/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.603/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.603/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=2300.00, TE=2.98, TI=900.00, flip angle=9.00 i_ras = (-1, 2.8871e-08, 6.89179e-08) j_ras = (1.00583e-07, -1.30967e-09, -1) k_ras = (-5.21541e-08, 1, -2.76486e-10) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.603/nu0.mnc... -------------------------------------------------------- Iteration 1 Wed Aug 29 10:56:49 CDT 2012 nu_correct -clobber ./tmp.mri_nu_correct.mni.603/nu0.mnc ./tmp.mri_nu_correct.mni.603/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.603/0/ [drg@qnode0362:/projects/d20277/dek/PPMI/done/3157/mri/] [2012-08-29 10:56:49] running: /projects/d20277/software/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.603/0/ ./tmp.mri_nu_correct.mni.603/nu0.mnc ./tmp.mri_nu_correct.mni.603/nu1.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 50 CV of field change: 0.00123115 [drg@qnode0362:/projects/d20277/dek/PPMI/done/3157/mri/] [2012-08-29 10:57:33] running: /projects/d20277/software/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.603/nu0.mnc ./tmp.mri_nu_correct.mni.603/0//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done -------------------------------------------------------- Iteration 2 Wed Aug 29 10:57:37 CDT 2012 nu_correct -clobber ./tmp.mri_nu_correct.mni.603/nu1.mnc ./tmp.mri_nu_correct.mni.603/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.603/1/ [drg@qnode0362:/projects/d20277/dek/PPMI/done/3157/mri/] [2012-08-29 10:57:38] running: /projects/d20277/software/freesurfer/mni/bin/nu_estimate_np_and_em -parzen -log -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir ./tmp.mri_nu_correct.mni.603/1/ ./tmp.mri_nu_correct.mni.603/nu1.mnc ./tmp.mri_nu_correct.mni.603/nu2.imp Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done 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Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Processing:.................................................................Done Number of iterations: 30 CV of field change: 0.000989746 [drg@qnode0362:/projects/d20277/dek/PPMI/done/3157/mri/] [2012-08-29 10:58:05] running: /projects/d20277/software/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.603/nu1.mnc ./tmp.mri_nu_correct.mni.603/1//template.mnc Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.603/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.603/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /projects/d20277/dek/PPMI/done/3157/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.603/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.603/ones.mgz sysname Linux hostname qnode0362 machine x86_64 user drg input ./tmp.mri_nu_correct.mni.603/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.603/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 Found 16777216 values in range Counting number of voxels Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.603/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.603/sum.junk --avgwf ./tmp.mri_nu_correct.mni.603/input.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.603/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.603/sum.junk --avgwf ./tmp.mri_nu_correct.mni.603/input.mean.dat sysname Linux hostname qnode0362 machine x86_64 user drg Loading ./tmp.mri_nu_correct.mni.603/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.603/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.603/ones.mgz --i ./tmp.mri_nu_correct.mni.603/nu2.mnc --sum ./tmp.mri_nu_correct.mni.603/sum.junk --avgwf ./tmp.mri_nu_correct.mni.603/output.mean.dat $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.603/ones.mgz --i ./tmp.mri_nu_correct.mni.603/nu2.mnc --sum ./tmp.mri_nu_correct.mni.603/sum.junk --avgwf ./tmp.mri_nu_correct.mni.603/output.mean.dat sysname Linux hostname qnode0362 machine x86_64 user drg Loading ./tmp.mri_nu_correct.mni.603/ones.mgz Loading ./tmp.mri_nu_correct.mni.603/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 1.67772e+07 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.603/output.mean.dat mris_calc -o ./tmp.mri_nu_correct.mni.603/nu2.mnc ./tmp.mri_nu_correct.mni.603/nu2.mnc mul 1.09899238567690775597 Saving result to './tmp.mri_nu_correct.mni.603/nu2.mnc' (type = MINC ) [ ok ] mri_convert ./tmp.mri_nu_correct.mni.603/nu2.mnc nu.mgz --like orig.mgz mri_convert ./tmp.mri_nu_correct.mni.603/nu2.mnc nu.mgz --like orig.mgz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from ./tmp.mri_nu_correct.mni.603/nu2.mnc... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 2.8871e-08, 6.89179e-08) j_ras = (1.00583e-07, -1.30967e-09, -1) k_ras = (-5.21541e-08, 1, -2.76486e-10) INFO: transform src into the like-volume: orig.mgz Reslicing using trilinear interpolation writing to nu.mgz... mri_make_uchar nu.mgz transforms/talairach.xfm nu.mgz type change took 0 minutes and 9 seconds. mapping ( 6, 98) to ( 3, 110) Wed Aug 29 10:59:07 CDT 2012 mri_nu_correct.mni done #-------------------------------------------- #@# Intensity Normalization Wed Aug 29 10:59:07 CDT 2012 /projects/d20277/dek/PPMI/done/3157/mri mri_normalize -g 1 nu.mgz T1.mgz using max gradient = 1.000 reading from nu.mgz... normalizing image... building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to T1.mgz 3D bias adjustment took 3 minutes and 42 seconds. MRIsplineNormalize(): npeaks = 14 Starting OpenSpline(): npoints = 14 white matter peak found at 111 white matter peak found at 104 gm peak at 42 (42), valley at 19 (19) csf peak at 21, setting threshold to 35 white matter peak found at 111 white matter peak found at 110 gm peak at 41 (41), valley at 20 (20) csf peak at 21, setting threshold to 34 #-------------------------------------------- #@# Skull Stripping Wed Aug 29 11:02:50 CDT 2012 /projects/d20277/dek/PPMI/done/3157/mri mri_watershed -T1 -brain_atlas /projects/d20277/software/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) gcaAllocMax: node dims 64 64 64 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=149 y=207 z=128 r=108 first estimation of the main basin volume: 5344590 voxels Looking for seedpoints 2 found in the cerebellum 1 found in the rest of the brain global maximum in x=110, y=172, z=166, Imax=255 CSF=11, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 10 percent done. Analyze... main basin size=3756879712 voxels, voxel volume =1.000 = 3756879712 mmm3 = 3756879.616 cm3 done. PostAnalyze...Basin Prior 11 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=127,y=107, z=125, r=9168 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=5, CSF_MAX=23 , nb = 44370 RIGHT_CER CSF_MIN=0, CSF_intensity=5, CSF_MAX=32 , nb = 3186 LEFT_CER CSF_MIN=0, CSF_intensity=4, CSF_MAX=26 , nb = 2700 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=5, CSF_MAX=21 , nb = 19908 LEFT_BRAIN CSF_MIN=0, CSF_intensity=4, CSF_MAX=23 , nb = 18216 OTHER CSF_MIN=1, CSF_intensity=15, CSF_MAX=29 , nb = 360 mri_watershed Error: GLOBAL region of the brain empty ! Linux qnode0362 2.6.18-128.el5-perfctr #1 SMP Wed Jun 23 11:22:11 CDT 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 3157 exited with ERRORS at Wed Aug 29 11:03:03 CDT 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting New invocation of recon-all Wed Aug 29 11:18:54 CDT 2012 /projects/d20277/dek/PPMI/done/3157 /projects/d20277/software/freesurfer/bin/recon-all -skullstrip -no-wsgcaatlas -s 3157 subjid 3157 setenv SUBJECTS_DIR /projects/d20277/dek/PPMI/done FREESURFER_HOME /projects/d20277/software/freesurfer Actual FREESURFER_HOME /projects/d20277/software/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux quser03 2.6.18-274.17.1.el5 #1 SMP Wed Jan 4 22:45:44 EST 2012 x86_64 x86_64 x86_64 GNU/Linux cputime 2:00:00 filesize unlimited datasize unlimited stacksize 10240 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 524288 kbytes maxproc 409600 total used free shared buffers cached Mem: 49431948 4148688 45283260 0 464244 599208 -/+ buffers/cache: 3085236 46346712 Swap: 50331636 0 50331636 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 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: 2012/08/29-16:18:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 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: 2012/08/29-16:18:54-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.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 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:55-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:56-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:57-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:58-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:59-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:59-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:59-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:59-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:59-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:59-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:18:59-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: drg Machine: quser03 Platform: Linux PlatformVersion: 2.6.18-274.17.1.el5 CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /projects/d20277/software/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /projects/d20277/software/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /projects/d20277/software/freesurfer Previous: /usr/local/freesurfer #-------------------------------------------- #@# Skull Stripping Wed Aug 29 11:19:00 CDT 2012 /projects/d20277/dek/PPMI/done/3157/mri mri_watershed -T1 T1.mgz brainmask.auto.mgz Mode: T1 normalized volume ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz *************************WATERSHED************************** Sorting... T1-weighted MRI image modification of the preflooding height to 15 percent Count how many 110 voxels are present : 181804 Find the largest 110-component... heap usage = 823412 Kbytes. removing small segments (less than 1 percent of maxarea).done And identify it as the main brain basin...done Main component: 106266 voxels first estimation of the COG coord: x=128 y=143 z=122 r=85 first estimation of the main basin volume: 2658567 voxels global maximum in x=214, y=204, z=204, Imax=255 CSF=14, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 15 percent done. Analyze... main basin size= 2585476 voxels, voxel volume =1.000 = 2585476 mmm3 = 2585.476 cm3 done. PostAnalyze... ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin ambiguous basin, non merged: 7 ambiguous voxels; size: 432 voxels done. ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=121,y=158, z=142, r=156161 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4 , nb = 40338 Problem with the least square interpolation in GM_MIN calculation. CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 4, 5, 22, 40 after analyzing : 4, 18, 25, 23 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...111 iterations *********************VALIDATION********************* curvature mean = -0.010, std = 0.018 curvature mean = 77.157, std = 18.089 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 15.41, sigma = 30.11 after rotation: sse = 15.41, sigma = 30.11 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 20.27, its var is 26.17 before Erosion-Dilatation 27.62% of inacurate vertices after Erosion-Dilatation 35.87% of inacurate vertices 48.91% of 'positive' inacurate vertices 51.09% of 'negative' inacurate vertices The surface validation has detected a possible Error If the final segmentation is not valid, try using the option '-atlas' Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...44 iterations mri_strip_skull: done peeling brain Brain Size = 2178472 voxels, voxel volume = 1.000 mm3 = 2178472 mmm3 = 2178.472 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------------ recon-all -s 3157 finished without error at Wed Aug 29 11:19:29 CDT 2012 New invocation of recon-all Wed Aug 29 11:21:46 CDT 2012 /projects/d20277/dek/PPMI/done/3157 /projects/d20277/software/freesurfer/bin/recon-all -sd /home/drg/myprojects/dek/PPMI/done -autorecon2-wm -autorecon3 -subjid 3157 subjid 3157 setenv SUBJECTS_DIR /projects/d20277/dek/PPMI/done FREESURFER_HOME /projects/d20277/software/freesurfer Actual FREESURFER_HOME /projects/d20277/software/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Linux qnode0516 2.6.18-128.el5-perfctr #1 SMP Wed Jun 23 11:22:11 CDT 2010 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize unlimited coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked unlimited maxproc 409600 total used free shared buffers cached Mem: 49432648 21557432 27875216 0 256 11656404 -/+ buffers/cache: 9900772 39531876 Swap: 0 0 0 ######################################## program versions used $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 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: 2012/08/29-16:21:47-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 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: 2012/08/29-16:21:47-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr 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 2010-02-20 at 17:32:37 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:47-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:47-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize.c,v 1.73 2011/03/11 20:55:38 fischl Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:47-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_watershed.cpp,v 1.96 2011/03/16 21:23:49 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:47-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:47-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:48-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_label2label.c,v 1.40.2.1 2011/05/19 17:21:56 greve Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:48-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_em_register.c,v 1.84 2011/03/16 21:23:48 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:48-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_normalize.c,v 1.52 2011/03/02 00:04:14 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:48-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_register.c,v 1.78 2011/03/02 14:27:40 fischl Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:48-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_ca_label.c,v 1.96 2011/03/02 00:04:13 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:48-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:48-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:48-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:48-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:49-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:49-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:49-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:49-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:49-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:49-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:49-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:49-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:49-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_euler_number.c,v 1.8 2011/03/02 00:04:32 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:50-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_make_surfaces.c,v 1.127 2011/03/02 00:04:33 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:50-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:50-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:50-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:50-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:50-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:50-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mris_calc.c,v 1.37.2.4 2011/04/04 00:53:08 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ ProgramName: mri_robust_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:50-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_register.cpp,v 1.52 2011/03/16 21:23:49 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:50-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:51-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:51-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:51-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2012/08/29-16:21:51-GMT BuildTimeStamp: May 22 2011 08:23:31 CVS: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ User: drg Machine: qnode0516 Platform: Linux PlatformVersion: 2.6.18-128.el5-perfctr CompilerName: GCC CompilerVersion: 30400 ####################################### GCADIR /projects/d20277/software/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /projects/d20277/software/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### INFO: current FREESURFER_HOME does not match that of previous processing. Current: /projects/d20277/software/freesurfer Previous: /usr/local/freesurfer #-------------------------------------------- #@# Mask BFS Wed Aug 29 11:21:52 CDT 2012 /projects/d20277/dek/PPMI/done/3157/mri mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz threshold mask volume at 5 mghRead(/projects/d20277/dek/PPMI/done/3157/mri/brain.mgz, -1): could not open file mri_mask: could not read source volume brain.mgz Linux qnode0516 2.6.18-128.el5-perfctr #1 SMP Wed Jun 23 11:22:11 CDT 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 3157 exited with ERRORS at Wed Aug 29 11:21:52 CDT 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting