Hello,
I just added version 5.3 to our system and am trying run recon-all on our dataset but it seems to be failing for all subjects pretty early. The only error I see is in the output (below) is: "bc: error while loading shared libraries: libreadline.so.5: cannot open shared object file: No such file or directory". Is libreadline.so.5 supposed to be a part of the freesurfer package? Or is it something that should already exist on most systems? If its a later than I will speak to our system admins.
Thank you, Erin
Fri May 24 13:58:33 EDT 2013 /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618 /home/t/tpaus/raleong/freesurfer/bin/recon-all -subject fam1002_122618 -i /scratch/t/tpaus/edickie/slsj_parents_T1Wc/fam1002_122618/fam1002_122618_T1Wsc.nii -sd /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/ -all subjid fam1002_122618 setenv SUBJECTS_DIR /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524 FREESURFER_HOME /home/t/tpaus/raleong/freesurfer Actual FREESURFER_HOME /home/t/tpaus/raleong/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux gpc-f146n031 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 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 20000 memorylocked unlimited maxproc 257772
total used free shared buffers cached Mem: 33002388 2099240 30903148 0 0 508072 -/+ buffers/cache: 1591168 31411220 Swap: 0 0 0
######################################## 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: 2013/05/24-17:58:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.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: 2013/05/24-17:58:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.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: 2013/05/24-17:58:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.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: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.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: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /home/t/tpaus/raleong/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /home/t/tpaus/raleong/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618
mri_convert /scratch/t/tpaus/edickie/slsj_parents_T1Wc/fam1002_122618/fam1002_122618_T1Wsc.nii /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig/001.mgz
mri_convert /scratch/t/tpaus/edickie/slsj_parents_T1Wc/fam1002_122618/fam1002_122618_T1Wsc.nii /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /scratch/t/tpaus/edickie/slsj_parents_T1Wc/fam1002_122618/fam1002_122618_T1Wsc.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.998083, -0.0436341, -0.0438852) j_ras = (0.0442841, 0.998922, 0.0139487) k_ras = (0.0432293, -0.0158654, 0.998939) writing to /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Fri May 24 13:58:59 EDT 2013 Found 1 runs /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/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 /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig/001.mgz /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/rawavg.mgz
/scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618
mri_convert /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/rawavg.mgz /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig.mgz --conform
mri_convert /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/rawavg.mgz /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.998083, -0.0436341, -0.0438852) j_ras = (0.0442841, 0.998922, 0.0139487) k_ras = (0.0432293, -0.0158654, 0.998939) Original Data has (1, 0.5, 0.5) mm size and (192, 512, 350) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig.mgz...
mri_add_xform_to_header -c /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/transforms/talairach.xfm /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig.mgz /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig.mgz
INFO: extension is mgz #-------------------------------------------- #@# Talairach Fri May 24 13:59:31 EDT 2013 /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/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
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#-------------------------------------------- #@# Talairach Failure Detection Fri May 24 14:00:51 EDT 2013 /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7230, pval=0.4932 >= threshold=0.0050)
awk -f /home/t/tpaus/raleong/freesurfer/bin/extract_talairach_avi_QA.awk /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/transforms/talairach_avi.log
tal_QC_AZS /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/transforms/talairach_avi.log
TalAviQA: 0.97680 z-score: #-------------------------------------------- #@# Nu Intensity Correction Fri May 24 14:00:52 EDT 2013
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
/scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri /home/t/tpaus/raleong/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 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux gpc-f146n031 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Fri May 24 14:00:52 EDT 2013 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.9181 /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9181/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9181/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 5.2969e-09, 3.72529e-09) j_ras = (0, 3.72529e-09, -1) k_ras = (-1.57161e-09, 1, -1.86265e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.9181/nu0.mnc...
-------------------------------------------------------- Iteration 1 Fri May 24 14:00:54 EDT 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.9181/nu0.mnc ./tmp.mri_nu_correct.mni.9181/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.9181/0/ [edickie@gpc-f146n031:/scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/] [2013-05-24 14:00:54] running: /home/t/tpaus/raleong/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.9181/0/ ./tmp.mri_nu_correct.mni.9181/nu0.mnc ./tmp.mri_nu_correct.mni.9181/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 Number of iterations: 14 CV of field change: 0.000993178 [edickie@gpc-f146n031:/scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/] [2013-05-24 14:01:05] running: /home/t/tpaus/raleong/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.9181/nu0.mnc ./tmp.mri_nu_correct.mni.9181/0//template.mnc
Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done
-------------------------------------------------------- Iteration 2 Fri May 24 14:01:10 EDT 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.9181/nu1.mnc ./tmp.mri_nu_correct.mni.9181/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.9181/1/ [edickie@gpc-f146n031:/scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/] [2013-05-24 14:01:10] running: /home/t/tpaus/raleong/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.9181/1/ ./tmp.mri_nu_correct.mni.9181/nu1.mnc ./tmp.mri_nu_correct.mni.9181/nu2.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 Number of iterations: 12 CV of field change: 0.000932884 [edickie@gpc-f146n031:/scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/] [2013-05-24 14:01:20] running: /home/t/tpaus/raleong/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.9181/nu1.mnc ./tmp.mri_nu_correct.mni.9181/1//template.mnc
Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done
mri_binarize --i ./tmp.mri_nu_correct.mni.9181/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9181/ones.mgz
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.9181/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9181/ones.mgz sysname Linux hostname gpc-f146n031 machine x86_64 user edickie
input ./tmp.mri_nu_correct.mni.9181/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.9181/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.9181/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9181/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9181/input.mean.dat
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9181/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9181/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9181/input.mean.dat sysname Linux hostname gpc-f146n031 machine x86_64 user edickie UseRobust 0 Loading ./tmp.mri_nu_correct.mni.9181/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 16777216.000
Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.9181/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9181/ones.mgz --i ./tmp.mri_nu_correct.mni.9181/nu2.mnc --sum ./tmp.mri_nu_correct.mni.9181/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9181/output.mean.dat
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9181/ones.mgz --i ./tmp.mri_nu_correct.mni.9181/nu2.mnc --sum ./tmp.mri_nu_correct.mni.9181/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9181/output.mean.dat sysname Linux hostname gpc-f146n031 machine x86_64 user edickie UseRobust 0 Loading ./tmp.mri_nu_correct.mni.9181/ones.mgz Loading ./tmp.mri_nu_correct.mni.9181/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000
Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.9181/output.mean.dat mri_segstats done bc: error while loading shared libraries: libreadline.so.5: cannot open shared object file: No such file or directory mris_calc -o ./tmp.mri_nu_correct.mni.9181/nu2.mnc ./tmp.mri_nu_correct.mni.9181/nu2.mnc mul Linux gpc-f146n031 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s fam1002_122618 exited with ERRORS at Fri May 24 14:01:44 EDT 2013
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Hello Erin,
libreadline.so is not distributed as part of freesurfer, it should be located somewhere on your system. For example, on CentOS 64bit platforms it can be found in the "/lib64" directory. And on 32bit platforms it can be found in the "/usr/lib" directory. Do you see anything that looks like libreadline.so in either of those directories on your system"?
-Zeke
On 05/24/2013 03:44 PM, Erin W. E. Dickie wrote:
Hello,
I just added version 5.3 to our system and am trying run recon-all on our dataset but it seems to be failing for all subjects pretty early. The only error I see is in the output (below) is: "bc: error while loading shared libraries: libreadline.so.5: cannot open shared object file: No such file or directory". Is libreadline.so.5 supposed to be a part of the freesurfer package? Or is it something that should already exist on most systems? If its a later than I will speak to our system admins.
Thank you, Erin
Fri May 24 13:58:33 EDT 2013 /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618 /home/t/tpaus/raleong/freesurfer/bin/recon-all -subject fam1002_122618 -i /scratch/t/tpaus/edickie/slsj_parents_T1Wc/fam1002_122618/fam1002_122618_T1Wsc.nii -sd /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/ -all subjid fam1002_122618 setenv SUBJECTS_DIR /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524 FREESURFER_HOME /home/t/tpaus/raleong/freesurfer Actual FREESURFER_HOME /home/t/tpaus/raleong/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux gpc-f146n031 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 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 20000 memorylocked unlimited maxproc 257772
total used free shared buffers cachedMem: 33002388 2099240 30903148 0 0 508072 -/+ buffers/cache: 1591168 31411220 Swap: 0 0 0
######################################## 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: 2013/05/24-17:58:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.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: 2013/05/24-17:58:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.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: 2013/05/24-17:58:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.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: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.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: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /home/t/tpaus/raleong/freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.gca AvgCurvTif average.curvature.filled.buckner40.tif GCSDIR /home/t/tpaus/raleong/freesurfer/average GCS curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs ####################################### /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618
mri_convert /scratch/t/tpaus/edickie/slsj_parents_T1Wc/fam1002_122618/fam1002_122618_T1Wsc.nii /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig/001.mgz
mri_convert /scratch/t/tpaus/edickie/slsj_parents_T1Wc/fam1002_122618/fam1002_122618_T1Wsc.nii /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /scratch/t/tpaus/edickie/slsj_parents_T1Wc/fam1002_122618/fam1002_122618_T1Wsc.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.998083, -0.0436341, -0.0438852) j_ras = (0.0442841, 0.998922, 0.0139487) k_ras = (0.0432293, -0.0158654, 0.998939) writing to /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Fri May 24 13:58:59 EDT 2013 Found 1 runs /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/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 /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig/001.mgz /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/rawavg.mgz
/scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618
mri_convert /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/rawavg.mgz /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig.mgz --conform
mri_convert /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/rawavg.mgz /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.998083, -0.0436341, -0.0438852) j_ras = (0.0442841, 0.998922, 0.0139487) k_ras = (0.0432293, -0.0158654, 0.998939) Original Data has (1, 0.5, 0.5) mm size and (192, 512, 350) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig.mgz...
mri_add_xform_to_header -c /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/transforms/talairach.xfm /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig.mgz /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/orig.mgz
INFO: extension is mgz #-------------------------------------------- #@# Talairach Fri May 24 13:59:31 EDT 2013 /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/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
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#-------------------------------------------- #@# Talairach Failure Detection Fri May 24 14:00:51 EDT 2013 /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7230, pval=0.4932 >= threshold=0.0050)
awk -f /home/t/tpaus/raleong/freesurfer/bin/extract_talairach_avi_QA.awk /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/transforms/talairach_avi.log
tal_QC_AZS /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/transforms/talairach_avi.log
TalAviQA: 0.97680 z-score: #-------------------------------------------- #@# Nu Intensity Correction Fri May 24 14:00:52 EDT 2013
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
/scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri /home/t/tpaus/raleong/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 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux gpc-f146n031 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Fri May 24 14:00:52 EDT 2013 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.9181 /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9181/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9181/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 5.2969e-09, 3.72529e-09) j_ras = (0, 3.72529e-09, -1) k_ras = (-1.57161e-09, 1, -1.86265e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.9181/nu0.mnc...
Iteration 1 Fri May 24 14:00:54 EDT 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.9181/nu0.mnc ./tmp.mri_nu_correct.mni.9181/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.9181/0/ [edickie@gpc-f146n031:/scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/] [2013-05-24 14:00:54] running: /home/t/tpaus/raleong/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.9181/0/ ./tmp.mri_nu_correct.mni.9181/nu0.mnc ./tmp.mri_nu_correct.mni.9181/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 Number of iterations: 14 CV of field change: 0.000993178 [edickie@gpc-f146n031:/scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/] [2013-05-24 14:01:05] running: /home/t/tpaus/raleong/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.9181/nu0.mnc ./tmp.mri_nu_correct.mni.9181/0//template.mnc
Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done
Iteration 2 Fri May 24 14:01:10 EDT 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.9181/nu1.mnc ./tmp.mri_nu_correct.mni.9181/nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.9181/1/ [edickie@gpc-f146n031:/scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/] [2013-05-24 14:01:10] running: /home/t/tpaus/raleong/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.9181/1/ ./tmp.mri_nu_correct.mni.9181/nu1.mnc ./tmp.mri_nu_correct.mni.9181/nu2.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 Number of iterations: 12 CV of field change: 0.000932884 [edickie@gpc-f146n031:/scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri/] [2013-05-24 14:01:20] running: /home/t/tpaus/raleong/freesurfer/mni/bin/make_template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.9181/nu1.mnc ./tmp.mri_nu_correct.mni.9181/1//template.mnc
Transforming slices:......................................................................................Done Transforming slices:................................................................................................................................................................................................................................................................Done mri_binarize --i ./tmp.mri_nu_correct.mni.9181/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9181/ones.mgz
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /scratch/t/tpaus/edickie/slsj_parents_Freesurfer5_20130524/fam1002_122618/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.9181/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9181/ones.mgz sysname Linux hostname gpc-f146n031 machine x86_64 user edickie
input ./tmp.mri_nu_correct.mni.9181/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.9181/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.9181/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9181/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9181/input.mean.dat
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9181/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9181/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9181/input.mean.dat sysname Linux hostname gpc-f146n031 machine x86_64 user edickie UseRobust 0 Loading ./tmp.mri_nu_correct.mni.9181/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 16777216.000
Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.9181/input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9181/ones.mgz --i ./tmp.mri_nu_correct.mni.9181/nu2.mnc --sum ./tmp.mri_nu_correct.mni.9181/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9181/output.mean.dat
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9181/ones.mgz --i ./tmp.mri_nu_correct.mni.9181/nu2.mnc --sum ./tmp.mri_nu_correct.mni.9181/sum.junk --avgwf ./tmp.mri_nu_correct.mni.9181/output.mean.dat sysname Linux hostname gpc-f146n031 machine x86_64 user edickie UseRobust 0 Loading ./tmp.mri_nu_correct.mni.9181/ones.mgz Loading ./tmp.mri_nu_correct.mni.9181/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000
Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.9181/output.mean.dat mri_segstats done bc: error while loading shared libraries: libreadline.so.5: cannot open shared object file: No such file or directory mris_calc -o ./tmp.mri_nu_correct.mni.9181/nu2.mnc ./tmp.mri_nu_correct.mni.9181/nu2.mnc mul Linux gpc-f146n031 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s fam1002_122618 exited with ERRORS at Fri May 24 14:01:44 EDT 2013
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yes I see it in /lib64. So I just need to add /lib64 to the PATH and it should work? Thanks, Erin
On Fri, May 24, 2013 at 4:18 PM, Z K zkaufman@nmr.mgh.harvard.edu wrote:
Hello Erin,
libreadline.so is not distributed as part of freesurfer, it should be located somewhere on your system. For example, on CentOS 64bit platforms it can be found in the "/lib64" directory. And on 32bit platforms it can be found in the "/usr/lib" directory. Do you see anything that looks like libreadline.so in either of those directories on your system"?
-Zeke
On 05/24/2013 03:44 PM, Erin W. E. Dickie wrote:
Hello,
I just added version 5.3 to our system and am trying run recon-all on our dataset but it seems to be failing for all subjects pretty early. The only error I see is in the output (below) is: "bc: error while loading shared libraries: libreadline.so.5: cannot open shared object file: No such file or directory". Is libreadline.so.5 supposed to be a part of the freesurfer package? Or is it something that should already exist on most systems? If its a later than I will speak to our system admins.
Thank you, Erin
Fri May 24 13:58:33 EDT 2013 /scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524/** fam1002_122618 /home/t/tpaus/raleong/**freesurfer/bin/recon-all -subject fam1002_122618 -i /scratch/t/tpaus/edickie/slsj_**parents_T1Wc/fam1002_122618/** fam1002_122618_T1Wsc.nii -sd /scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524/ -all subjid fam1002_122618 setenv SUBJECTS_DIR /scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524 FREESURFER_HOME /home/t/tpaus/raleong/**freesurfer Actual FREESURFER_HOME /home/t/tpaus/raleong/**freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_**64-stable-pub-v5.3.0 Linux gpc-f146n031 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 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 20000 memorylocked unlimited maxproc 257772
total used free shared buffers cachedMem: 33002388 2099240 30903148 0 0 508072 -/+ buffers/cache: 1591168 31411220 Swap: 0 0 0
##############################**########## 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: 2013/05/24-17:58:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.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: 2013/05/24-17:58:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.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: 2013/05/24-17:58:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.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: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.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: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ##############################**######### GCADIR /home/t/tpaus/raleong/**freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.**gca AvgCurvTif average.curvature.filled.**buckner40.tif GCSDIR /home/t/tpaus/raleong/**freesurfer/average GCS curvature.buckner40.filled.**desikan_killiany.2010-03-25.**gcs ##############################**######### /scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524/** fam1002_122618
mri_convert /scratch/t/tpaus/edickie/slsj_**parents_T1Wc/fam1002_122618/** fam1002_122618_T1Wsc.nii /scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524/** fam1002_122618/mri/orig/001.**mgz
mri_convert /scratch/t/tpaus/edickie/slsj_**parents_T1Wc/fam1002_122618/** fam1002_122618_T1Wsc.nii /scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524/** fam1002_122618/mri/orig/001.**mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /scratch/t/tpaus/edickie/slsj_**parents_T1Wc/fam1002_122618/** fam1002_122618_T1Wsc.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.998083, -0.0436341, -0.0438852) j_ras = (0.0442841, 0.998922, 0.0139487) k_ras = (0.0432293, -0.0158654, 0.998939) writing to /scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524/** fam1002_122618/mri/orig/001.**mgz... #-----------------------------**--------------- #@# MotionCor Fri May 24 13:58:59 EDT 2013 Found 1 runs /scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524/** fam1002_122618/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 /scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524/** fam1002_122618/mri/orig/001.**mgz /scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524/** fam1002_122618/mri/rawavg.mgz
/scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524/** fam1002_122618
mri_convert /scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524/** fam1002_122618/mri/rawavg.mgz /scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524/** fam1002_122618/mri/orig.mgz --conform
mri_convert /scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524/** fam1002_122618/mri/rawavg.mgz /scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524/** fam1002_122618/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524/** fam1002_122618/mri/rawavg.mgz.**.. TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.998083, -0.0436341, -0.0438852) j_ras = (0.0442841, 0.998922, 0.0139487) k_ras = (0.0432293, -0.0158654, 0.998939) Original Data has (1, 0.5, 0.5) mm size and (192, 512, 350) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524/** fam1002_122618/mri/orig.mgz...
mri_add_xform_to_header -c /scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524/** fam1002_122618/mri/transforms/**talairach.xfm /scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524/** fam1002_122618/mri/orig.mgz /scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524/** fam1002_122618/mri/orig.mgz
INFO: extension is mgz #-----------------------------**--------------- #@# Talairach Fri May 24 13:59:31 EDT 2013 /scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524/** fam1002_122618/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
cp transforms/talairach.auto.xfm transforms/talairach.xfm
#-----------------------------**--------------- #@# Talairach Failure Detection Fri May 24 14:00:51 EDT 2013 /scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524/** fam1002_122618/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm
talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7230, pval=0.4932 >= threshold=0.0050)
awk -f /home/t/tpaus/raleong/**freesurfer/bin/extract_**talairach_avi_QA.awk /scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524/** fam1002_122618/mri/transforms/**talairach_avi.log
tal_QC_AZS /scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524/** fam1002_122618/mri/transforms/**talairach_avi.log
TalAviQA: 0.97680 z-score: #-----------------------------**--------------- #@# Nu Intensity Correction Fri May 24 14:00:52 EDT 2013
mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2
/scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524/** fam1002_122618/mri /home/t/tpaus/raleong/**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 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux gpc-f146n031 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Fri May 24 14:00:52 EDT 2013 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.9181 /scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524/** fam1002_122618/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9181/**nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9181/**nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 5.2969e-09, 3.72529e-09) j_ras = (0, 3.72529e-09, -1) k_ras = (-1.57161e-09, 1, -1.86265e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.9181/**nu0.mnc... ------------------------------**-------------------------- Iteration 1 Fri May 24 14:00:54 EDT 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.9181/**nu0.mnc ./tmp.mri_nu_correct.mni.9181/**nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.9181/**0/ [edickie@gpc-f146n031:/**scratch/t/tpaus/edickie/slsj_** parents_Freesurfer5_20130524/**fam1002_122618/mri/] [2013-05-24 14:00:54] running: /home/t/tpaus/raleong/**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.9181/**0/ ./tmp.mri_nu_correct.mni.9181/**nu0.mnc ./tmp.mri_nu_correct.mni.9181/** 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 Number of iterations: 14 CV of field change: 0.000993178 [edickie@gpc-f146n031:/**scratch/t/tpaus/edickie/slsj_** parents_Freesurfer5_20130524/**fam1002_122618/mri/] [2013-05-24 14:01:05] running: /home/t/tpaus/raleong/**freesurfer/mni/bin/make_**template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.9181/**nu0.mnc ./tmp.mri_nu_correct.mni.9181/**0//template.mnc
Transforming slices:.......................**..............................** ..............................**...Done Transforming slices:.......................**..............................** ..............................**..............................** ..............................**..............................** ..............................**..............................** .......................Done ------------------------------**-------------------------- Iteration 2 Fri May 24 14:01:10 EDT 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.9181/**nu1.mnc ./tmp.mri_nu_correct.mni.9181/**nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.9181/**1/ [edickie@gpc-f146n031:/**scratch/t/tpaus/edickie/slsj_** parents_Freesurfer5_20130524/**fam1002_122618/mri/] [2013-05-24 14:01:10] running: /home/t/tpaus/raleong/**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.9181/**1/ ./tmp.mri_nu_correct.mni.9181/**nu1.mnc ./tmp.mri_nu_correct.mni.9181/** nu2.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 Number of iterations: 12 CV of field change: 0.000932884 [edickie@gpc-f146n031:/**scratch/t/tpaus/edickie/slsj_** parents_Freesurfer5_20130524/**fam1002_122618/mri/] [2013-05-24 14:01:20] running: /home/t/tpaus/raleong/**freesurfer/mni/bin/make_**template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.9181/**nu1.mnc ./tmp.mri_nu_correct.mni.9181/**1//template.mnc
Transforming slices:.......................**..............................** ..............................**...Done Transforming slices:.......................**..............................** ..............................**..............................** ..............................**..............................** ..............................**..............................** .......................Done mri_binarize --i ./tmp.mri_nu_correct.mni.9181/**nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9181/**ones.mgz
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /scratch/t/tpaus/edickie/slsj_**parents_Freesurfer5_20130524/** fam1002_122618/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.9181/**nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9181/**ones.mgz sysname Linux hostname gpc-f146n031 machine x86_64 user edickie
input ./tmp.mri_nu_correct.mni.9181/**nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.9181/**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.9181/**ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9181/**sum.junk --avgwf ./tmp.mri_nu_correct.mni.9181/**input.mean.dat
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9181/** ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9181/**sum.junk --avgwf ./tmp.mri_nu_correct.mni.9181/**input.mean.dat sysname Linux hostname gpc-f146n031 machine x86_64 user edickie UseRobust 0 Loading ./tmp.mri_nu_correct.mni.9181/**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 16777216.000
Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.9181/**input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9181/**ones.mgz --i ./tmp.mri_nu_correct.mni.9181/**nu2.mnc --sum ./tmp.mri_nu_correct.mni.9181/**sum.junk --avgwf ./tmp.mri_nu_correct.mni.9181/**output.mean.dat
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9181/** ones.mgz --i ./tmp.mri_nu_correct.mni.9181/**nu2.mnc --sum ./tmp.mri_nu_correct.mni.9181/**sum.junk --avgwf ./tmp.mri_nu_correct.mni.9181/**output.mean.dat sysname Linux hostname gpc-f146n031 machine x86_64 user edickie UseRobust 0 Loading ./tmp.mri_nu_correct.mni.9181/**ones.mgz Loading ./tmp.mri_nu_correct.mni.9181/**nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000
Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.9181/**output.mean.dat mri_segstats done bc: error while loading shared libraries: libreadline.so.5: cannot open shared object file: No such file or directory mris_calc -o ./tmp.mri_nu_correct.mni.9181/**nu2.mnc ./tmp.mri_nu_correct.mni.9181/**nu2.mnc mul Linux gpc-f146n031 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s fam1002_122618 exited with ERRORS at Fri May 24 14:01:44 EDT 2013
To report a problem, see http://surfer.nmr.mgh.harvard.**edu/fswiki/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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Not quite... What is the ouput when you type "ls -l libreadline*" in the /lib64 directory?
On 05/24/2013 04:23 PM, Erin W. E. Dickie wrote:
Yes I see it in /lib64. So I just need to add /lib64 to the PATH and it should work? Thanks, Erin
On Fri, May 24, 2013 at 4:18 PM, Z K <zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu> wrote:
Hello Erin, libreadline.so is not distributed as part of freesurfer, it should be located somewhere on your system. For example, on CentOS 64bit platforms it can be found in the "/lib64" directory. And on 32bit platforms it can be found in the "/usr/lib" directory. Do you see anything that looks like libreadline.so in either of those directories on your system"? -Zeke On 05/24/2013 03:44 PM, Erin W. E. Dickie wrote: Hello, I just added version 5.3 to our system and am trying run recon-all on our dataset but it seems to be failing for all subjects pretty early. The only error I see is in the output (below) is: "bc: error while loading shared libraries: libreadline.so.5: cannot open shared object file: No such file or directory". Is libreadline.so.5 supposed to be a part of the freesurfer package? Or is it something that should already exist on most systems? If its a later than I will speak to our system admins. Thank you, Erin Fri May 24 13:58:33 EDT 2013 /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618 /home/t/tpaus/raleong/__freesurfer/bin/recon-all -subject fam1002_122618 -i /scratch/t/tpaus/edickie/slsj___parents_T1Wc/fam1002_122618/__fam1002_122618_T1Wsc.nii -sd /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/ -all subjid fam1002_122618 setenv SUBJECTS_DIR /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524 FREESURFER_HOME /home/t/tpaus/raleong/__freesurfer Actual FREESURFER_HOME /home/t/tpaus/raleong/__freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86___64-stable-pub-v5.3.0 Linux gpc-f146n031 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 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 20000 memorylocked unlimited maxproc 257772 total used free shared buffers cached Mem: 33002388 2099240 30903148 0 0 508072 -/+ buffers/cache: 1591168 31411220 Swap: 0 0 0 ##############################__########## 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: 2013/05/24-17:58:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.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: 2013/05/24-17:58:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.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: 2013/05/24-17:58:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.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: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuter Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.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: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ##############################__######### GCADIR /home/t/tpaus/raleong/__freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.__gca AvgCurvTif average.curvature.filled.__buckner40.tif GCSDIR /home/t/tpaus/raleong/__freesurfer/average GCS curvature.buckner40.filled.__desikan_killiany.2010-03-25.__gcs ##############################__######### /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618 mri_convert /scratch/t/tpaus/edickie/slsj___parents_T1Wc/fam1002_122618/__fam1002_122618_T1Wsc.nii /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/orig/001.__mgz mri_convert /scratch/t/tpaus/edickie/slsj___parents_T1Wc/fam1002_122618/__fam1002_122618_T1Wsc.nii /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/orig/001.__mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /scratch/t/tpaus/edickie/slsj___parents_T1Wc/fam1002_122618/__fam1002_122618_T1Wsc.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.998083, -0.0436341, -0.0438852) j_ras = (0.0442841, 0.998922, 0.0139487) k_ras = (0.0432293, -0.0158654, 0.998939) writing to /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/orig/001.__mgz... #-----------------------------__--------------- #@# MotionCor Fri May 24 13:58:59 EDT 2013 Found 1 runs /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/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 /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/orig/001.__mgz /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/rawavg.mgz /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618 mri_convert /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/rawavg.mgz /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/orig.mgz --conform mri_convert /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/rawavg.mgz /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/rawavg.mgz.__.. TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.998083, -0.0436341, -0.0438852) j_ras = (0.0442841, 0.998922, 0.0139487) k_ras = (0.0432293, -0.0158654, 0.998939) Original Data has (1, 0.5, 0.5) mm size and (192, 512, 350) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/orig.mgz... mri_add_xform_to_header -c /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/transforms/__talairach.xfm /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/orig.mgz /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/orig.mgz INFO: extension is mgz #-----------------------------__--------------- #@# Talairach Fri May 24 13:59:31 EDT 2013 /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/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 cp transforms/talairach.auto.xfm transforms/talairach.xfm #-----------------------------__--------------- #@# Talairach Failure Detection Fri May 24 14:00:51 EDT 2013 /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7230, pval=0.4932 >= threshold=0.0050) awk -f /home/t/tpaus/raleong/__freesurfer/bin/extract___talairach_avi_QA.awk /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/transforms/__talairach_avi.log tal_QC_AZS /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/transforms/__talairach_avi.log TalAviQA: 0.97680 z-score: #-----------------------------__--------------- #@# Nu Intensity Correction Fri May 24 14:00:52 EDT 2013 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri /home/t/tpaus/raleong/__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 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux gpc-f146n031 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Fri May 24 14:00:52 EDT 2013 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.9181 /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9181/__nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9181/__nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 5.2969e-09, 3.72529e-09) j_ras = (0, 3.72529e-09, -1) k_ras = (-1.57161e-09, 1, -1.86265e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.9181/__nu0.mnc... ------------------------------__-------------------------- Iteration 1 Fri May 24 14:00:54 EDT 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.9181/__nu0.mnc ./tmp.mri_nu_correct.mni.9181/__nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.9181/__0/ [edickie@gpc-f146n031:/__scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/] [2013-05-24 14:00:54] running: /home/t/tpaus/raleong/__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.9181/__0/ ./tmp.mri_nu_correct.mni.9181/__nu0.mnc ./tmp.mri_nu_correct.mni.9181/__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 Number of iterations: 14 CV of field change: 0.000993178 [edickie@gpc-f146n031:/__scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/] [2013-05-24 14:01:05] running: /home/t/tpaus/raleong/__freesurfer/mni/bin/make___template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.9181/__nu0.mnc ./tmp.mri_nu_correct.mni.9181/__0//template.mnc Transforming slices:.......................__..............................__..............................__...Done Transforming slices:.......................__..............................__..............................__..............................__..............................__..............................__..............................__..............................__.......................Done ------------------------------__-------------------------- Iteration 2 Fri May 24 14:01:10 EDT 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.9181/__nu1.mnc ./tmp.mri_nu_correct.mni.9181/__nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.9181/__1/ [edickie@gpc-f146n031:/__scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/] [2013-05-24 14:01:10] running: /home/t/tpaus/raleong/__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.9181/__1/ ./tmp.mri_nu_correct.mni.9181/__nu1.mnc ./tmp.mri_nu_correct.mni.9181/__nu2.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 Number of iterations: 12 CV of field change: 0.000932884 [edickie@gpc-f146n031:/__scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri/] [2013-05-24 14:01:20] running: /home/t/tpaus/raleong/__freesurfer/mni/bin/make___template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.9181/__nu1.mnc ./tmp.mri_nu_correct.mni.9181/__1//template.mnc Transforming slices:.......................__..............................__..............................__...Done Transforming slices:.......................__..............................__..............................__..............................__..............................__..............................__..............................__..............................__.......................Done mri_binarize --i ./tmp.mri_nu_correct.mni.9181/__nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9181/__ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /scratch/t/tpaus/edickie/slsj___parents_Freesurfer5_20130524/__fam1002_122618/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.9181/__nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9181/__ones.mgz sysname Linux hostname gpc-f146n031 machine x86_64 user edickie input ./tmp.mri_nu_correct.mni.9181/__nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.9181/__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.9181/__ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9181/__sum.junk --avgwf ./tmp.mri_nu_correct.mni.9181/__input.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9181/__ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9181/__sum.junk --avgwf ./tmp.mri_nu_correct.mni.9181/__input.mean.dat sysname Linux hostname gpc-f146n031 machine x86_64 user edickie UseRobust 0 Loading ./tmp.mri_nu_correct.mni.9181/__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 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.9181/__input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9181/__ones.mgz --i ./tmp.mri_nu_correct.mni.9181/__nu2.mnc --sum ./tmp.mri_nu_correct.mni.9181/__sum.junk --avgwf ./tmp.mri_nu_correct.mni.9181/__output.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9181/__ones.mgz --i ./tmp.mri_nu_correct.mni.9181/__nu2.mnc --sum ./tmp.mri_nu_correct.mni.9181/__sum.junk --avgwf ./tmp.mri_nu_correct.mni.9181/__output.mean.dat sysname Linux hostname gpc-f146n031 machine x86_64 user edickie UseRobust 0 Loading ./tmp.mri_nu_correct.mni.9181/__ones.mgz Loading ./tmp.mri_nu_correct.mni.9181/__nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.9181/__output.mean.dat mri_segstats done bc: error while loading shared libraries: libreadline.so.5: cannot open shared object file: No such file or directory mris_calc -o ./tmp.mri_nu_correct.mni.9181/__nu2.mnc ./tmp.mri_nu_correct.mni.9181/__nu2.mnc mul Linux gpc-f146n031 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s fam1002_122618 exited with ERRORS at Fri May 24 14:01:44 EDT 2013 To report a problem, see http://surfer.nmr.mgh.harvard.__edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> _________________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.__edu/mailman/listinfo/__freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> The information in this e-mail is intended only for the person to whom it is addressed. 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I get this....
lrwxrwxrwx 1 root root 18 May 4 09:49 libreadline.so.5 -> libreadline.so.5.2 -rwxr-xr-x 1 root root 261144 Nov 10 2010 libreadline.so.5.2 lrwxrwxrwx 1 root root 18 May 4 09:49 libreadline.so.6 -> libreadline.so.6.0 -rwxr-xr-x 1 root root 269592 Jun 22 2012 libreadline.so.6.0
On Fri, May 24, 2013 at 4:28 PM, Z K zkaufman@nmr.mgh.harvard.edu wrote:
Not quite... What is the ouput when you type "ls -l libreadline*" in the /lib64 directory?
On 05/24/2013 04:23 PM, Erin W. E. Dickie wrote:
Yes I see it in /lib64. So I just need to add /lib64 to the PATH and it should work? Thanks, Erin
On Fri, May 24, 2013 at 4:18 PM, Z K <zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.**harvard.edu zkaufman@nmr.mgh.harvard.edu>> wrote:
Hello Erin, libreadline.so is not distributed as part of freesurfer, it should be located somewhere on your system. For example, on CentOS 64bit platforms it can be found in the "/lib64" directory. And on 32bit platforms it can be found in the "/usr/lib" directory. Do you see anything that looks like libreadline.so in either of those directories on your system"? -Zeke On 05/24/2013 03:44 PM, Erin W. E. Dickie wrote: Hello, I just added version 5.3 to our system and am trying run recon-all on our dataset but it seems to be failing for all subjects pretty early. The only error I see is in the output (below) is: "bc: error while loading shared libraries: libreadline.so.5: cannot open shared object file: No such file or directory". Islibreadline.so.5 supposed to be a part of the freesurfer package? Or is it something that should already exist on most systems? If its a later than I will speak to our system admins.
Thank you, Erin Fri May 24 13:58:33 EDT 2013 /scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_**20130524/__fam1002_122618 /home/t/tpaus/raleong/__**freesurfer/bin/recon-all -subject fam1002_122618 -i /scratch/t/tpaus/edickie/slsj_**__parents_T1Wc/fam1002_122618/** __fam1002_122618_T1Wsc.nii -sd /scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_**20130524/ -all subjid fam1002_122618 setenv SUBJECTS_DIR /scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_20130524 FREESURFER_HOME /home/t/tpaus/raleong/__**freesurfer Actual FREESURFER_HOME /home/t/tpaus/raleong/__**freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86__** _64-stable-pub-v5.3.0
Linux gpc-f146n031 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 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 20000 memorylocked unlimited maxproc 257772 total used free shared buffers cached Mem: 33002388 2099240 30903148 0 0 508072 -/+ buffers/cache: 1591168 31411220 Swap: 0 0 0 ##############################**__########## 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: 2013/05/24-17:58:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.72012/09/05 21:55:16 mreuter Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.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: 2013/05/24-17:58:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.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: 2013/05/24-17:58:33-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize.c,v 1.73.2.1 2012/10/17 19:11:32 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_watershed.cpp,v 1.96.2.1 2011/11/08 22:18:44 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segment.c,v 1.40 2011/03/02 00:04:24 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_label2label.c,v 1.40.2.2 2013/04/02 16:26:15 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400
======= NUMBER OF OPENMP THREADS = 1 ======= ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:34-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_em_register.c,v 1.84.2.3 2013/02/09 00:49:26 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion:40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_normalize.c,v 1.52.2.2 2012/10/17 19:11:32 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_register.c,v 1.78.2.3 2013/02/09 00:42:20 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_ca_label.c,v 1.96.2.1 2012/08/28 22:11:20 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_pretess.c,v 1.20 2011/03/02 00:04:23 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:35-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fill.c,v 1.118 2011/03/16 21:23:49 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_tessellate.c,v 1.36 2011/03/02 00:04:25 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_concatenate_lta.c,v 1.10 2011/03/16 21:23:48 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_smooth.c,v 1.28 2011/03/02 00:04:34 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_inflate.c,v 1.43 2011/03/02 00:04:32 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:36-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_sphere.c,v 1.57 2011/03/02 00:04:34 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_fix_topology.c,v 1.48 2011/03/02 00:04:32 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_ca_label.c,v 1.35 2011/03/02 00:04:27 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_euler_number.c,v 1.8.2.2 2013/01/14 22:40:07 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_make_surfaces.c,v 1.127.2.6 2013/05/12 22:28:01 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:37-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_volmask.cpp,v 1.25 2011/03/02 00:04:34 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_anatomical_stats.c,v 1.72 2011/03/02 00:04:26 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:38-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mrisp_paint.c,v 1.11 2011/03/02 00:04:35 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_curvature_stats.c,v 1.64 2011/03/02 00:04:30 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mris_calc.c,v 1.37.2.8 2013/01/28 17:05:17 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.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: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_register.cpp,v 1.52.2.3 2012/11/20 17:26:47 mreuterExp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.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: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuterExp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:39-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_or.c,v 1.3 2011/03/02 00:04:13 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/05/24-17:58:40-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ User: edickie Machine: gpc-f146n031 Platform: Linux PlatformVersion: 2.6.32-358.2.1.el6.x86_64 CompilerName: GCC CompilerVersion: 40400 ##############################**__######### GCADIR /home/t/tpaus/raleong/__**freesurfer/average GCA RB_all_2008-03-26.gca GCASkull RB_all_withskull_2008-03-26.__**gca AvgCurvTif average.curvature.filled.__**buckner40.tif GCSDIR /home/t/tpaus/raleong/__**freesurfer/average GCS curvature.buckner40.filled.__**desikan_killiany.2010-03-25.__ **gcs ##############################**__######### /scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_** 20130524/__fam1002_122618
mri_convert /scratch/t/tpaus/edickie/slsj_**__parents_T1Wc/fam1002_122618/**__fam1002_122618_T1Wsc.nii /scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_** 20130524/__fam1002_122618/mri/**orig/001.__mgz
mri_convert /scratch/t/tpaus/edickie/slsj_**__parents_T1Wc/fam1002_122618/**__fam1002_122618_T1Wsc.nii /scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_** 20130524/__fam1002_122618/mri/**orig/001.__mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /scratch/t/tpaus/edickie/slsj_**__parents_T1Wc/fam1002_122618/**__fam1002_122618_T1Wsc.nii...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.998083, -0.0436341, -0.0438852) j_ras = (0.0442841, 0.998922, 0.0139487) k_ras = (0.0432293, -0.0158654, 0.998939) writing to /scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_**20130524/__fam1002_122618/mri/**orig/001.__mgz... #-----------------------------**__---------------
#@# MotionCor Fri May 24 13:58:59 EDT 2013 Found 1 runs /scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_**20130524/__fam1002_122618/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 /scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_**20130524/__fam1002_122618/mri/**orig/001.__mgz /scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_** 20130524/__fam1002_122618/mri/**rawavg.mgz
/scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_**20130524/__fam1002_122618
mri_convert /scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_**20130524/__fam1002_122618/mri/**rawavg.mgz /scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_** 20130524/__fam1002_122618/mri/**orig.mgz --conform
mri_convert /scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_**20130524/__fam1002_122618/mri/**rawavg.mgz /scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_** 20130524/__fam1002_122618/mri/**orig.mgz
--conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_**20130524/__fam1002_122618/mri/**rawavg.mgz.__..
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.998083, -0.0436341, -0.0438852) j_ras = (0.0442841, 0.998922, 0.0139487) k_ras = (0.0432293, -0.0158654, 0.998939) Original Data has (1, 0.5, 0.5) mm size and (192, 512, 350)voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_** 20130524/__fam1002_122618/mri/**orig.mgz...
mri_add_xform_to_header -c /scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_**20130524/__fam1002_122618/mri/**transforms/__talairach.xfm /scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_** 20130524/__fam1002_122618/mri/**orig.mgz /scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_** 20130524/__fam1002_122618/mri/**orig.mgz
INFO: extension is mgz #-----------------------------**__--------------- #@# Talairach Fri May 24 13:59:31 EDT 2013 /scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_**20130524/__fam1002_122618/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 --xfmtransforms/talairach.auto.xfm
cp transforms/talairach.auto.xfm transforms/talairach.xfm #-----------------------------**__--------------- #@# Talairach Failure Detection Fri May 24 14:00:51 EDT 2013 /scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_**20130524/__fam1002_122618/mri
talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7230, pval=0.4932 >= threshold=0.0050) awk -f /home/t/tpaus/raleong/__**freesurfer/bin/extract___**talairach_avi_QA.awk /scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_** 20130524/__fam1002_122618/mri/**transforms/__talairach_avi.log
tal_QC_AZS /scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_**20130524/__fam1002_122618/mri/**transforms/__talairach_avi.log
TalAviQA: 0.97680 z-score: #-----------------------------**__--------------- #@# Nu Intensity Correction Fri May 24 14:00:52 EDT 2013 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_**20130524/__fam1002_122618/mri /home/t/tpaus/raleong/__**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 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux gpc-f146n031 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux Fri May 24 14:00:52 EDT 2013 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.9181 /scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_**20130524/__fam1002_122618/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9181/**__nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.9181/**__nu0.mnc
-odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 5.2969e-09, 3.72529e-09) j_ras = (0, 3.72529e-09, -1) k_ras = (-1.57161e-09, 1, -1.86265e-09) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.9181/**__nu0.mnc... ------------------------------**__-------------------------- Iteration 1 Fri May 24 14:00:54 EDT 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.9181/**__nu0.mnc ./tmp.mri_nu_correct.mni.9181/**__nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.9181/**__0/ [edickie@gpc-f146n031:/__**scratch/t/tpaus/edickie/slsj__**_parents_Freesurfer5_20130524/**__fam1002_122618/mri/]
[2013-05-24 14:00:54] running: /home/t/tpaus/raleong/__**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.9181/**__0/ ./tmp.mri_nu_correct.mni.9181/**__nu0.mnc ./tmp.mri_nu_correct.mni.9181/**__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
Number of iterations: 14 CV of field change: 0.000993178 [edickie@gpc-f146n031:/__**scratch/t/tpaus/edickie/slsj__**_parents_Freesurfer5_20130524/**__fam1002_122618/mri/]
[2013-05-24 14:01:05] running: /home/t/tpaus/raleong/__**freesurfer/mni/bin/make___**template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.9181/**__nu0.mnc ./tmp.mri_nu_correct.mni.9181/**__0//template.mnc
Transforming slices:.......................**__............................**..__..........................**....__...Done Transforming slices:.......................**__............................** ..__..........................**....__........................** ......__......................**........__....................** ..........__..................**............__................** ..............__..............**.........Done ------------------------------**__--------------------------
Iteration 2 Fri May 24 14:01:10 EDT 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.9181/**__nu1.mnc ./tmp.mri_nu_correct.mni.9181/**__nu2.mnc -tmpdir ./tmp.mri_nu_correct.mni.9181/**__1/ [edickie@gpc-f146n031:/__**scratch/t/tpaus/edickie/slsj__**_parents_Freesurfer5_20130524/**__fam1002_122618/mri/]
[2013-05-24 14:01:10] running: /home/t/tpaus/raleong/__**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.9181/**__1/ ./tmp.mri_nu_correct.mni.9181/**__nu1.mnc ./tmp.mri_nu_correct.mni.9181/**__nu2.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
Number of iterations: 12 CV of field change: 0.000932884 [edickie@gpc-f146n031:/__**scratch/t/tpaus/edickie/slsj__**_parents_Freesurfer5_20130524/**__fam1002_122618/mri/]
[2013-05-24 14:01:20] running: /home/t/tpaus/raleong/__**freesurfer/mni/bin/make___**template -quiet -shrink 3 ./tmp.mri_nu_correct.mni.9181/**__nu1.mnc ./tmp.mri_nu_correct.mni.9181/**__1//template.mnc
Transforming slices:.......................**__............................**..__..........................**....__...Done Transforming slices:.......................**__............................** ..__..........................**....__........................** ......__......................**........__....................** ..........__..................**............__................** ..............__..............**.........Done mri_binarize --i ./tmp.mri_nu_correct.mni.9181/**__nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9181/**__ones.mgz
$Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /scratch/t/tpaus/edickie/slsj_**__parents_Freesurfer5_**20130524/__fam1002_122618/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.9181/** __nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.9181/**__ones.mgz
sysname Linux hostname gpc-f146n031 machine x86_64 user edickie input ./tmp.mri_nu_correct.mni.9181/**__nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.9181/**__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.9181/**__ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9181/**__sum.junk --avgwf ./tmp.mri_nu_correct.mni.9181/**__input.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9181/**__ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.9181/**__sum.junk--avgwf ./tmp.mri_nu_correct.mni.9181/**__input.mean.dat
sysname Linux hostname gpc-f146n031 machine x86_64 user edickie UseRobust 0 Loading ./tmp.mri_nu_correct.mni.9181/**__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 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.9181/**__input.mean.dat mri_segstats done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9181/**__ones.mgz --i ./tmp.mri_nu_correct.mni.9181/**__nu2.mnc --sum ./tmp.mri_nu_correct.mni.9181/**__sum.junk --avgwf ./tmp.mri_nu_correct.mni.9181/**__output.mean.dat $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.9181/**__ones.mgz --i ./tmp.mri_nu_correct.mni.9181/**__nu2.mnc --sum ./tmp.mri_nu_correct.mni.9181/**__sum.junk --avgwf ./tmp.mri_nu_correct.mni.9181/**__output.mean.dat sysname Linux hostname gpc-f146n031 machine x86_64 user edickie UseRobust 0 Loading ./tmp.mri_nu_correct.mni.9181/**__ones.mgz Loading ./tmp.mri_nu_correct.mni.9181/**__nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 16777216 16777216.000 Reporting on 1 segmentations Computing spatial average of each frame 0 Writing to ./tmp.mri_nu_correct.mni.9181/**__output.mean.dat mri_segstats done bc: error while loading shared libraries: libreadline.so.5: cannot open shared object file: No such file or directory mris_calc -o ./tmp.mri_nu_correct.mni.9181/**__nu2.mnc ./tmp.mri_nu_correct.mni.9181/**__nu2.mnc mul Linux gpc-f146n031 2.6.32-358.2.1.el6.x86_64 #1 SMP Wed Mar 13 00:26:49 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s fam1002_122618 exited with ERRORS at Fri May 24 14:01:44 EDT 2013 To report a problem, see http://surfer.nmr.mgh.harvard.**__edu/fswiki/BugReporting <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>______________________________**___________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>https://mail.nmr.mgh.harvard._**_edu/mailman/listinfo/__**freesurfer
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Erin W. E. Dickie -
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